Although it may seem like the other species are evil to us, our species could just as likely seem evil to them. The only reason we assume that the Guardians and the citizens of the city are the righteous ones is the fact that we have the bias of playing from their perspective. On the other hand, our enemies never attack us; we attack them. Sure, there have been those times when we have missions where "nothing is more important now" because we're all about to die etc., but all of that knowledge has simply been fed to us by the Speaker or our Ghosts. The truly reliable unbiased sources of knowledge are the Grimoire cards and Bungie. The Grimoire cards hint many times, or sometimes say blatantly, that the Traveler and the Guardians are not in fact good. Bungie has never officially said anything about our intentions either other than the fact that we're working to help the Traveler and the people of the city. That could mean many different things.