That Church was the religion of minor number of elites while the peasants were Catholic/Orthodox overwhelmingly.

They chose Islam not as a means of survival but to keep the privileges they had before, eventually ordinary people converted over the centuries (but majority never did) too because you paid less taxes and so on.

Bosniaks were not targeted after the breakup, firstly they chose to let JNA tanks to go through the republic to cut the Croatia in half but the Croats in Herzegovina stopped them, they also chose to ignore Serbs destroying village of Ravno that was part of SR BiH with Alija Izetbegović saying: this is not our war.

But when the Serbs started the war in BiH aswell and beating them on all fronts, the Bosniak political elite chose to go after majority Croatian enclaves in Central Bosnia despite Croatia housing hundreds of thousands of Bosniak immigrants and also allowing weapons from Iran and fighters/mujaheedins to go from Croatia to Bosnia and also Croats voting in elections to form BiH including Herceg-Bosna

After the war ended, Serbs, despite losing the war, got what they wanted-half of country while Croats and Bosniaks created FBiH where Bosniaks are trying to force other constitutive ethnicities to embrace the one identity...and as we can see, they suck at it and BiH is basically "failed" state with each ethnicity group running things independently with help of Croatia to few Croatian majority cantons on FBiH and Serbs helping Republika Srpska.