Well, is the destroying of his home planet optional or not? I'm not against being the hero, but do I always have to be a lawful good hero?
In Disgaea you were an antihero, which was a very nice change. However, you were still not able to change your alignment based on your own choices.
The only things I see that touch this subject is personal relationships between the playable characters, but their choices don't change the outcome of subquest very much at all.
Non-partyleader: "Let's go here, what do you say, Mr. Leader?"
*Player gets to choose yer or no.*
Partyleader: "I want to do this instead!"
Non-partyleader: "But that's not smart, go there anyway, else something bad will happen to innocent NPCs"
Partyleader: "OKAY! :("

-edit-
This was in reply to Zeromus' post.

Also, I can see that the example I used would be smart if the NPC in question was crucial to the story. But in very many cases, that is not the case.

It could be fun to end up with different conversations at the final showdown too. Such as a main character filled with feelings of hate and revenge towards the villain versus one that fights for justice and a better world.