I would alter the soul destruction to what it was originally: your soul turns to evil. I think Larian put in soul destruction as a) substitute for alignment not thinking about the implications and b) a reasons to have Withers involved.
So I agree with @Mictheltjuhn (on *something* -
Withers wouldn't say we haven't changed since Withers cares about souls above all else; this is his reason for opposing the dead three. While he prefers Kelmvor he was able to work with the the three in the past. The soul destruction plan changed that attitude.
The need for a mind flayer in the final act needs to be changed.
The only reason its' there is to encourage people to use tadpole powers on a replay.