What reforms do I suggest be made. Well for one when we look at how the Qur'an values not taking innocent lives:
The Qu'ran only values not taking innocent Muslim lives. The killing of infidels are recommended all through the Qu'ran. Aren't non-Muslim lives innocent?
4:89 SHAKIR: They desire that you should disbelieve as they have disbelieved, so that you might be (all) alike; therefore take not from among them friends until they fly (their homes) in Allah's way; but if they turn back,
then seize them and kill them wherever you find them, and take not from among them a friend or a helper.
Here Allah says those who disbelieve must be seized and killed. Could this also include apostasy?
9:5 SHAKIR: So when the sacred months have passed away,
then slay the idolaters wherever you find them, and take them captives and besiege them and lie in wait for them in every ambush, then if they repent and keep up prayer and pay the poor-rate, leave their way free to them; surely Allah is Forgiving, Merciful.
9:29 SHAKIR: Fight those who do not believe in Allah, nor in the latter day, nor do they prohibit what Allah and His Messenger have prohibited, nor follow the religion of truth, out of those who have been given the Book, until they pay the tax in acknowledgment of superiority and they are in a state of subjection.
9:11-12 If they repent, establish regular prayers, and practice regular charity, they are your brethren in faith. But if they violate their oaths after their covenant, and taunt you for your faith,
fight ye the chiefs of Unfaith: for their oaths are nothing to them.
Here the Qu'ran clearly recommends fighting those who violate their covenant with Allah ie apostates
Then there is the stoning of people guilty of Adultery. The Qur'an gives the punishment for that offense as being flogging, not stoning. The Sunnah only gives 4 accounts of someone being stoned to death for Adultery, however the person stoned was a married Jew man who confessed to the incident. Stoning for adultery was law for Jews, and I know of no Hadith that refers to a Muslim being stoned to death
I think if you dug a bit deeper into the Sunnah you would change your mind on the above statements.
Sahih Muslim 17:4214 Allah's Apostle called the Jews and said: What is the punishment that you find in your Book (Torah) as a prescribed punishment for adultery? They said: We blacken the face with coal and flog as a substitute punishment for stoning. Thereupon Allah's Messenger said: O Allah, I am the first to revive Thy command when they had made it dead. He then commanded and he the offender was stoned to death.
The Jews of the time had addressed the barbarity of such punishments by reducing their harshness. However Muhammad insisted that since it was ordained by the Abrahamic God, no relenting from His command was possible.
Sahih Bukhari 89:303 - A Bedouin came and said, "My son was a labourer for this man and committed illegal sexual intercourse with his wife." The Prophet said, "I shall judge between you according to Allah's Book! Your son shall receive one-hundred lashes and be exiled for one year. "O you, Unais!" The Prophet addressed a man, "Go in the morning to the wife of this man and stone her to death." So Unais went to her the next morning and stoned her to death.
Sahih Muslim 17:4191 ? Allah's Messenger said: Receive teaching from me. When an unmarried male commits adultery with an unmarried female they should receive one hundred lashes and banishment for one year. And in case of married male committing adultery with a married female, they shall receive one hundred lashes and be stoned to death.
Sahih Muslim 17:4194 ? 'Umar b. Khattab sat on the pulpit of Allah's Messenger and said: Allah sent Muhammad with truth and He sent down the Book upon him, and the verse of stoning was included in what was sent down to him. We recited it, retained it in our memory and understood it. Allah's Messenger awarded the punishment of stoning to death and, after him we also awarded the punishment of stoning. I am afraid that with the lapse of time, the people may forget it and thus go astray by abandoning this duty prescribed by Allah. Stoning is a duty laid down in Allah's Book for married men and women who commit adultery.
Sahih Muslim 17:4198 - Jabir b. Samura reported: As he was being brought to Allah's Apostle I saw Malik, a short-statured person with strong sinews, having no cloak around him. He bore witness against his own self four times that he had committed adultery. He then got him stoned to death, and then delivered the address: Behold, as we set out for Jihad (holy war) in the cause of Allah, one of you lagged behind and shrieked like the bleating of a male goat. By Allah, in case I get hold of him, I shall certainly punish him.
Sahih Muslim 17:4201 - Allah's Apostle said: Is it true what has reached me about you? It has reached me that you have committed adultery with the slave-girl of so and so? He said: Yes. He (the narrator) said: He testified four times. He (the Prophet) then made pronouncement about him and he was stoned to death.
Sahih Muslim 17:4202 - Abu Sa'id reported that a person belonging to the clan of Aslam came to Allah's Messenger and said: I have committed immorality, so inflict punishment upon me. Allah's Apostle commanded us to stone him. We took him to the Baqi' al-Gharqad (the graveyard of Medina). We neither tied him nor dug any ditch for him. We attacked him with bones, with clods and pebbles. He ran away and we ran after him until he came upon the stony ground (al-Harra) and stopped there and we stoned him with heavy stones of the Harra until he became motionless.
Sahih Muslim 17:4205 - Then a woman of Ghamid came to him and said: Messenger of Allah, purify me, whereupon he said: What has happened to you? She said that she had become pregnant as a result of fornication. He said to her: You will not be punished until you deliver what is there in your womb. One of the Ansar (believers) became responsible for her until she was delivered of the child. He (that Ansari) came to Allah's Apostle and said the woman of Ghamid has given birth to a child. The Prophet said: In that case we shall not stone her and so leave her infant with none to suckle him.
Sahih Muslim 17:4206 - When she had weaned him, she came to him (the Prophet) with the child who was holding a piece of bread in his hand. She said: Allah's Apostle, here is he as I have weaned him and he eats food. He (the Prophet) entrusted the child to one of the Muslims and then pronounced punishment. And she was put in a ditch up to her chest and he commanded people and they stoned her. Khalid b Walid came forward with a stone which he flung at her head and there spurted blood on the face of Khalid and so he abused her. Allah's Apostle heard his (Khalid's) curse that he had hurried upon her. Thereupon he (the Prophet) said: Khalid, be gentle. By Him in Whose Hand is my life, she has made such a repentance that even if a wrongful tax-collector were to repent, he would have been forgiven. Then giving command regarding her, he prayed over her and she was buried.
Sahih Muslim 17:4207 - Imran b. Husain reported that a woman from Juhaina came to Allah's Apostle and she had become pregnant because of adultery. She said: Allah's Apostle, I have done something for which (prescribed punishment) must be imposed upon me, so impose that. Allah's Apostle called her master and said: Treat her well, and when she delivers bring her to me. He did accordingly. Then Allah's Apostle pronounced judgment about her and her clothes were tied around her and then he commanded and she was stoned to death.
Sahih Muslim 17:4211 - A Jew and a Jewess who had committed adultery were brought to Allah's Messenger. Allah's Messenger came to the Jews and said: What do you find in Torah for one who commits adultery? They said: We darken their faces and make them ride on the donkey with their faces turned to the opposite direction (and their backs touching each other), and then they are taken round the city. He said: Bring Torah if you are truthful. They brought it and recited it until when they came to the verse pertaining to stoning. Allah's Messenger pronounced judgment that both of them be stoned. Abdullah b.Umar said: I was one of those who stoned them, and I saw him (the Jew) protecting her (the Jewess) with his body.
Sahih Bukhari 82:803 - Narrated Ash-Sha'bi: from Ali when the latter stoned a lady to death on a Friday. Ali said, ?I have stoned her according to the tradition of Allah's Apostle.?
The way I was taught to understand this is that an apostate that was to be killed was a person who not only left Islam, but did it with the intention of going over to those who were at war with the Muslims and giving them aid. They had to be guilty of treason in other words. Today any apostate has a sentence of Death hanging over their head. Simply for thinking freely. This is what God created us to do. I may disagree with people leaving Islam, but that doesn't mean I should wish death upon them.
Abdullah, a scribe of Muhammad who wrote down verses as they were revealed ealizing that the revelations from Allah were contradictory, returned to Mecca and adopted his former religion. He did not take up arms against Muhammad. On conquest of Mecca Muhammad ordered Abdullah be killed
But the hadiths are filled with stories of apostates being killed when they did not fight against the Muslims. Muhammad himself recommends they be killed for no crime other than simply leaving the faith.
Sahih Bukhari 4:260 - Ali burnt some people and this news reached Ibn 'Abbas, who said, ?Had I been in his place I would not have burnt them, as the Prophet said, 'Don't punish (anybody) with Allah's Punishment (fire).' No doubt, I would have killed them, for the Prophet said, 'If somebody (a Muslim) discards his religion, kill him.'
Sunan Abu Da'ud 40:4747 - The Prophet said: "Soon there will appear disagreement and dissension in my people. They will swerve from the religion as an animal when shot at. They are worst of the people and are animals. Happy is the one who kills them and they kill him. He who fights against them will be nearer to Allah than others."
Sahih Bukhari 83:17 - Allah's Apostle said, "The blood of a Muslim who confesses that none has the right to be worshipped but Allah and that I am His Apostle, cannot be shed except in three cases: In retaliation for murder, a married person who commits illegal sexual intercourse and the one who reverts from Islam (apostate) and leaves the Muslims."
Sahih Bukhari 89:271 - Mu'adh asked, "What is wrong with this man?" Abu Musa replied, "He embraced Islam and then reverted back to Judaism." Mu'adh said, "I will not sit down unless you kill him as it is the verdict of Allah and His Apostle."
Sahih Muslim 16:4152 - Allah's Messenger said: It is not permissible to take the life of a Muslim who bears testimony that I am the Messenger of Allah, except in one of the three cases: the married adulterer, a life for life, and the deserter of Islam, abandoning the community.
Apologists might tell you one story but know death for leaving Islam as carried out by true Islamic societies is based soundly of the examples given by the prophet himself.