I think respeccing companions from the ground up is great.
I think it would be good to race and gender lock them but other then that, go nuts.
Shadowheart really does NOT have to be a cleric to be a devoted servant of Shar, there are 2 more classes with a very clear religious focus: Paladin and Monk
Wyll being a warlock may totally be erased, because his first few levels are probably not warlock and upon being transplanted with the illithid fetus, he lost his levels. It would actually make sense for him not to be a warlock level-wise, but still having a signed contract.
Gale being a wizard makes a lot of sense but lets not forget that he is a wizard frustrated by his loss of power. He could totally be roleplayed as reaching out for another source of strength out of desperation.
Lae'zel and Astarion really aren't defined by their classes, they could be literally anything and it would still work.