There should be if there isn't a hit to your good/evil rating if you just conqure one because you like their planet, at least the same as if you made one of the evil choices on one of the pop ups you occasionally get when you find a planet or random events. I can't find my good evil rating to be sure but I captured 3 minor races because they had better planets and didn't seem to effect my good rating with my good friends.... meaning same alignment friends or other independents that might be in danger.