Yes. Until he got full support from NATO who started bombing Serbian positions that sparked military advancements of joint Bosniak-Croat forces. Then he wanted to maximize the peace deal to his favor by making the Bosnian muslims lead the whole country.

Yes, that's exactly it. He wanted to keep Bosnia from splitting. I don't know if what he did was right or wrong but it wasn't illegal. And it doesn't make much sense that he would want Bosnia to be run by Muslims and yet have the first BiH Prime Minister be a Catholic (Croat).

Well, I would agree Serbs did crimes in easter Bosnia, killed and forced people to leave but let's not attribute it to one side only?

I was referring to Jovan Divjak. He was a Serb who was a general in the Bosnian Army. I was being sarcastic with the exterminating part.

It was motivated by nationalism and ethnic superiority complex on all sides and general distrust towards others. Here's what the document says that you provided talking about why some European governments were so relluctant to support ending of war in Bosnia: "To Holbrooke's list I would like to add a sixth factor: some European leaders were not eager to have a Muslim state in the heart of Balkans, fearing it might become a base for exporting extremism, a result that their neglect made more, not less, likely."
Alija's government created close ties with Iran prior to the dissintegration of Yugoslavia.

Alija could not strengthen ties between two countries where one didn't exist yet. And that quote is telling us that their lack of support for Bosnia resulted in a higher likelihood of extremism being planted in Bosnia. They weren't hasty because Bosnia was a base for Islamic extremism (it wasn't at the time), they feared that it would become one. But if we look today you can find more Islamic terrorist acts in the West than in Bosnia so they didn't get that one exactly right.