Alignments should be fluid. People change. The idea that going on a massive adventure, seeing the world, meeting interesting people, and killing some of them wouldn't change you at all is silly. Good people can become evil and vice versa. Well organized teetotalers can become sloppy drunks. Sane people can go crazy.
In PK, like so many other RPGs, your own alignment also changes in response to your actions in the game.
Being able to change companion alignments is nothing new either--you could do the same to Viconia. I think this kind of thing may just seem less dissonant in games without a quantifiable alignment system. For example, you could turn Alistair and Leliana a bit more evil/pragmatic in DA:O if you handled their companion quests in certain ways, and that made perfect sense.
