I have to come back to this thread now that I'm in Act 3, because I experienced what I would call "consequences."
To refuse becoming half-illithid was a DC 21 Wisdom Save on my character that was using tadpole powers.
There are also some minor dialogue lines that require rolls if you've been using the tadpole. For example:
If Jaheira asks you at Last Light if the tadpole is changing you, a character that hasn't used powers can say they're resisting with no roll, but one that has needs to roll Deception.
Yeah, I... uh... didn't make that important saving throw. I can only assume there will be more later, that will be even tougher now. We'll see how it plays out (no ending spoilers please)! My drow is not a nice guy, so if anyone deserves a bad end, it's him.