I'm aware of Izbegovic's Islamizing tendencies (and I never understood why the US and NATO decided to become allied with Izbegovic, other than perhaps as a gesture of good will to the Saudis), but the point is that his ideology would not have gotten the traction that it did without a civil war as a backdrop.
Of course the civil war might well not have started had it not been for at least some Bosniaks already having an animus against Serbs. (Remember among the south Slavs, religion is ethnicity.) The opening shots of the war were the machine gunning of a Serb wedding by Muslims. At that time I was a frequent poster on an Orthodox Christian discussion board on which another poster personally knew people at the wedding that was attacked.