Ok, so here's what I think:
I don't think it should be possible to "deliberately" (i.e. without meta-gaming) change a character's nature. This means there should be no clear dialogue choices that lead to this. You shouldn't actually know what is going on.
That being said, I believe that being on any kind of adventure or simply travelling together affects people. The choices you make during your quests should have a "visible" influence on your companions. They might not agree with things you do at first, but they might see that your methods reach results. Or your actions might make them see things in a different light. (For example something like: "You didn't kill this drow and now it turns out he/she (probably she thought : ] ) isn't actually that evil, I might have to rethink my lawful paladin-ways.") This shouldn't necessarily affect the whole nature of the companion, just a few little things, that might add up to something rather big and drastic. Of course this is very difficult to write, since it has to take a lot of little things into account and you might end up with contradicting statements. (I hated it so much in BG2 that after Anomen turned Chaotic Neutral his normal righteous dialogue would still trigger, although at the same time he was attacking Aerie, because she was too good.) And with a lot of those little things coming together why shouldn't the character change to something completely new; not at once just gradually shifting.