I disagree. Is substitutionary atonement open to interpretation in Christianity because a small cult disagrees with it?
Aha.
In a case like that, I'd say "Almost all of Group A believes in X, except for Group B, which considers itself part of Group A, although Group C within Group A considers them to be apostates."
Remember, as a nonbeliever, I view religions as belief systems. There is no True Word Of God against which to measure someone's beliefs, and therefor there is no Objectively True Christianity, or Objectively True Islam. As human creations, they're defined by humans.
Yes, they're tied to holy texts. Yes, the texts are generally static. Some parts seem pretty clear to an outsider, and some beliefs are fairly consistent throughout different groups/locations/times within a religion.
But trying to sort out a single, objectively defined philosophy from a holy text? If people who actually believe it's the word of God can't do it, I'm not going to pretend I can. Plus, I don't believe it's true anyway, which makes the task doubly moot.
If significant numbers of people who consider themselves to be part of the same religion disagree on an issue, then BY DEFINITION that issue doesn't disqualify someone from being a "real" Christian/Muslim/whatever. It is what they say it is. And if they disagree, then it's multiple things.
If you want to start making fatwas, it's a short ride until you have to decide whether the Sunnis or the Shiites aren't "real Muslims."
As for the Koran sanctioning the "killing of innocents," I have no idea. I haven't read it, and I'm not planning to. I would suspect the main source of intra-Islam disagreement is in the definition of "innocents."