Also remember that Angels are a step above humanity. They're immortal, almost entirely Lawful Good all the time, and are generally pretty close to being perfect beings. Most of them probably think they are perfect beings. Just because they are Lawful Good, and a handful of mortals happen to also be Lawful Good, does not mean they see eye-to-eye or even consider each other as allies. If you think about it, mortals are completely varied in alignment, a mortal can be good or evil easily. Mortals have a great capacity to do evil in the world, and Angels should realize this--meaning that there is no reason why Angels can't begin a campaign to rid the world of humanity. They cause too much evil for the piddly amount of good they bring, in the eyes of the Angels, and therefore for the greater good of the cosmos, they must be destroyed. Even good-aligned mortals are culled as well, because heaven knows when they'll swap sides of the alignment spectrum and wreak havoc.

Or alternatively, forget alignments of mortals entirely. Mortals cause a lot of problems, and always have. They only live a small amount of time, and they have no real foresight into the future. They act for the moment, and rarely consider the ramification of their actions, which can cause untold amounts of destruction to the universe. Think about how many eldritch abominations are let loose by unsuspecting or easily-fooled humanity. The Angels may have gotten tired of this, seeing the mortal races as just a blight to the universe. Ridding the world of these vermin is a good act to them, and therefore it's alright to slaughter them all.