I read somewhere that you could align yourself with bodhi?? I played the game as a lawful good paladin with 20 reputation. therefore this this idea was not an option. I was just curious to see what happens if you do so? how does it affect the storyline?

Well it affects it in a minor way, There quests change and you have to go againts the thives guild instead but dosen't change the whole story.

Not sure about the difference in EP, but you get some very useful equipment from siding with Bodhi.