I am not particularly fond of the alignment system, but the fact is, it has been there from the start, and as a consequenece it is used as a variable in many of our quests.
Regardless of how logic it is or isn't, it's one of the few variables we can use to send different players on different paths in a quest.
And the reason we do that is to at least in some small way counteract the Quest blabbing. Blabbing == when one stupid players tells some other stupid player in detail how to do a quest, so that their buddy or clannie or whatever can get the reward without doing anything to really earn it.
Other such variables that can be used in Quest scripts are Race, Class, Clan, stats like Int, Wis, Cha, Coolness etc. and to some extent Level and Tier too. Basically the Quest Mob would send a Centaur on a different path than a Martian, and might refuse totally to even talk to an evil aligned or low intelligence player.
So what everyone - and particularly coders - should bear in mind is, that if you mess with those basic elements, you also mess up an unspecified number of quests, which might be very hard to track down and fix.
That said, align should be at least resonably logic. It makes sense to me that if you specialize in fighting evil creatures, your align goes up, if you go around senselessly killing innocent women and children it goes down, and if you stick to hunting animals nothing big happens..