Not refuting the evidence since I'm torn whether or not Popo is evil, but you must consider something about the bird. At the end of episode one that bird distracts Vanilla so that Hyo-Hyo can get aboard the ship which indicates that it works for their organization. Though it's cliche he could have known that the bird would move him out of the way which is why he was willing to take that shot.
Then again, the way he unsteadily said "Are you alright" seems suspicious to me (though it could just be general surprise.)
I'm more curious about the gun that was next to Warp when he woke up. He was probably injured in a firefight.