We do have a fair number of plots which work like that... the consequences of your actions aren't always easily determined, and some only show up later on down the line.

I would like to point out one thing, though, for those who are worried: we have self-appointed "advocates" amongst the design team who put on their particular hat when they play through a game and want to ensure that their style of play is accomodated. This ranges from the intelligent evil guy to the smart-*** rogue to, yes, the paladin-esque do-gooder.
What they tend to look for, individually, is not that they always have an easily-identified option created just for them, but rather that the character they play always have a reasonable course of action available. After all, someone playing evil doesn't like being forced into gainless altruism any more than someone playing good likes being forced into doing terrible or heartless things. When I do quests, there should be a path that someone who believes they are good could try... it may not be the easiest path (and, indeed, that's a solid definition between morality and immorality) but it should be available and rewarding.