I would also like to let the companions level up as their creators intended. If I have to do it myself, everyone will end up more or less optimized and it's not the most interesting or fun route.
Its a tricky situation, i fully welcome the ability to respec and multiclass the companions. I like the ability to select my companions to my liking and to my character and i would feel a little "forced" to select a Companion becourse i "need" that particular class in my team somehow.
for more freedom the story around some companions probably "should" not have been created around "class" features but more about personal problems to be solved in the backstory.
one could still roleplay some sense into respeccing by arguing wyll is so desperate to get rid of the pact that he decides to follow a different path, or the Gale is so fed up with magic now (or lost it alsmost completely) that he decides to change careers also

Astarion has the least problem in my opinion, his story should work whether he is a rogue, cleric, wizard or even a paladin. His mission seems to be to get rid of his master, even a paladin could have been ambushed and turned into a vampire spawn.....