If the alignment system and the penalties for going evil are tough and balanced enough then it will work itself out. I think death penalties in which you lose skill and stat points and have to earn them back are the best systems to really work with the alignment system. Because systems where you just get them back over time don't work. If it's just like 45 minutes after you die untill you get them back then you can just organize your items or logout and make a sandwhich and it'll be over and you'll be fine again. You won't really feel it.
But this has been said so many times already in several different threads over several pages.