There isn't really a "good side" or "bad side" when it comes to the Order vs. the Noah (Allen is obviously the "good guy" because he's the protagonist, and everyone who opposes him is "bad"). Sure, the Noah have some weird goals that we may not like, but the Order isn't exactly perfect, and it looks like their motives may be called into question at some point, too. If they really wanted to protect humans, why would they treat their own underlings in such a manner? And remember, the title is "D.Gray
-Man"... seriously, isn't it better to have bad people on both sides rather than a clearly defined side of good and bad?