I could see it breaking characters. Making Wyll a Paladin might kill his backstory, but it's possible his bargain isn't tied to his class. Making Shadowheart a Cleric of Selune might cause story issues as well. And honestly who doesn't want to re-roll Lazael as a Bard.
I won't be changing the initial class of the companions as it could remove some of their interactions but if folks want to do it in their games I can't see how that could possibly matter to me.
