So it seems that mainstream (Sunni) Islam, or at least some aspects of said, regard Ismailism (the second branch of Shi'a Islam) as a heresy or not part of Islam.
So what would it take for Ismailism to actually be seen as a non-Muslim religion. Obviously the POD has to be after Islam is founded, but your challenge is to make it so Ismailism is its own separate religion and not a branch of Islam.
My own thoughts would be that it was something involving either the Qarmatians or the Fatimids, but it would be interesting to see your input. The Qarmatians did have many apostatical beliefs at times, so it could be something to do with them.
EDIT: And I apologize for yet another WI about obscure topics like this, it's just my interest du jour.