Palin has a right to her religious beliefs, as do fundamentalist Muslims who agree with her on so many issues of social policy. None of them has a right, however, to impose their beliefs on others by capturing and deploying the executive power of the state. The most noxious belief that Palin shares with Muslim fundamentalists is her conviction that faith is not a private affair of individuals but rather a moral imperative that believers should import into statecraft wherever they have the opportunity to do so. That is the point of her pledge to shape the judiciary. Such a theocratic impulse is incompatible with the Founding Fathers' commitment to tolerance and democracy, which is why they forbade the government to "establish" or officially support any particular religion or denomination.
McCain once excoriated the Rev. Jerry Falwell and his ilk as "agents of intolerance." That he took such a position gave his opposition to similar intolerance in Islam credibility. In light of his more recent disgraceful kowtowing to the Christian right, McCain's animus against fundamentalist Muslims no longer looks consistent. It looks bigoted and invidious. You can't say you are waging a war on religious extremism if you are trying to put a religious extremist a heartbeat away from the presidency.