First of all interesting title: 'The Trouble Is the West'
It is a long interview so let's quote the relevant texts only:
Reason: Should we acknowledge that organized religion has sometimes sparked precisely the kinds of emancipation movements that could lift Islam into modern times? Slavery in the United States ended in part because of opposition by prominent church members and the communities they galvanized. The Polish Catholic Church helped defeat the Jaruzelski puppet regime. Do you think Islam could bring about similar social and political changes?
Hirsi Ali: Only if Islam is defeated. Because right now, the political side of Islam, the power-hungry expansionist side of Islam, has become superior to the Sufis and the Ismailis and the peace-seeking Muslims.
Reason: Don’t you mean defeating radical Islam?
Hirsi Ali: No. Islam, period. Once it’s defeated, it can mutate into something peaceful. It’s very difficult to even talk about peace now. They’re not interested in peace.
Reason: We have to crush the world’s 1.5 billion Muslims under our boot? In concrete terms, what does that mean, “defeat Islam”?
Hirsi Ali: I think that we are at war with Islam. And there’s no middle ground in wars. Islam can be defeated in many ways. For starters, you stop the spread of the ideology itself; at present, there are native Westerners converting to Islam, and they’re the most fanatical sometimes. There is infiltration of Islam in the schools and universities of the West. You stop that. You stop the symbol burning and the effigy burning, and you look them in the eye and flex your muscles and you say, “This is a warning. We won’t accept this anymore.” There comes a moment when you crush your enemy.
Reason: Militarily?
Hirsi Ali: In all forms, and if you don’t do that, then you have to live with the consequence of being crushed.
Reason: Are we really heading toward anything so ominous?
Hirsi Ali: I think that’s where we’re heading. We’re heading there because the West has been in denial for a long time. It did not respond to the signals that were smaller and easier to take care of. Now we have some choices to make. This is a dilemma: Western civilization is a celebration of life—everybody’s life, even your enemy’s life. So how can you be true to that morality and at the same time defend yourself against a very powerful enemy that seeks to destroy you?
Reason: George Bush, not the most conciliatory person in the world, has said on plenty of occasions that we are not at war with Islam.
Hirsi Ali: If the most powerful man in the West talks like that, then, without intending to, he’s making radical Muslims think they’ve already won. There is no moderate Islam. There are Muslims who are passive, who don’t all follow the rules of Islam, but there’s really only one Islam, defined as submission to the will of God. There’s nothing moderate about it.
Reason: So when even a hard-line critic of Islam such as Daniel Pipes says, “Radical Islam is the problem, but moderate Islam is the solution,” he’s wrong?
Hirsi Ali: He’s wrong. Sorry about that.
There are parts of his opinions that I don't agree, like that
talking to Iran is a sheer waste of time and I would also think that she should accentuate the difference between Shia and Sunni Islam.
I will rephrase you question as: how do you advocate crushing a religion militarily without turning to violence towards its adherents?
Answer. You can't. Even a non-military approach will result in discriminatory polices toward its adherents. Problem is that if nothing is done(which is happening right now), what she says next (if you don’t do that, then you have to live with the consequence of being crushed) is very likely the outcome.
And because of this, people are advocating this kind of policies, opinions... Some are good people with good intentions, some are not. I remember one user here (TheWahhabist - which I much admire) who not so long ago said something like: "ISIS is the necessary evil". Problem with this is that given how much destruction ISIS has brought(in terms of everything), you could make a case that he doesn't care or even advocate violence. Which is not truth of course.
Point is, Islam is extreme and even good people with good intentions can sometimes advocate extreme ideas, ways... to counter its evilness.