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The "they're not real Muslims" argument is neither remarkable or new. The same argument is used by Christians all the time when inconvenient truths are raised. Like when you point out groups such as the "God Hates Fags" group, it's not uncommon at all to hear that "they're not real Christians". And it's the same story if you bring up the brutality of the Crusades or the Inquisition. This form of denial is not unique to Muslims at all, it's present among all ideologues regardless of the particular dogma they adhere to.
Likewise is the hedging when it concerns some central tenet of their faith. That's simply classic "ends justify the means logic" to which our very Christian president subscribes to. It concerns Bush not, that he had to lie to start the war in Iraq. He was so completely certain invading Iraq was the right thing to do that it didn't matter to him at all how he would go about doing it.
It's pointless to apologize for or try to rationalize this behavior. The real lesson is for us all to reject dogma regardless of it's form.