I think the alignment system is brilliant, and one of the core tenets of DnD. It would be a shame if it wasn't in the game. This COULD be the first Baldur's Gate game that does evil alignments right... Evil is self-serving, not outlandishly vile. Amusingly, I think many people actually play evil characters in games, who only wrongly believe themselves to be good. It's all about the rewards, rather than doing the right thing. If you could get an extra stat point by killing a random villager, most players would go for it in a heartbeat.
The problem is just that, almost always (certainly in both the Baldur's Gate games), doing the good thing also gives the best results, so there is no point in doing anything morally questionable. No (sane) evil character would do it!