So you're saying the "countdown clock" was in fact not a coincidence?
Anyway, I'm thinking that the joke here is that Melt is a real jerk, but we had really known that since the first series. That said:
In Melt's case: someone who doesn't know where his priorities lie. He's neither a good guy, nor a bad guy. He isn't even neutral either. I would say he's "nothing", but even he doesn't deserve that. One thing is certain, he doesn't deserve to be on Jil's team...he never did. On the other hand, Coopa is innocent because she was only following orders, plus she had no knowledge of what Melt was going to do.
After seeing all this happen, you would think that Melt might be the "third betrayal" that Ki mentioned in the first series, but I think this was too easy. I think we'll have to watch a little further before we can discern who the "third betrayal" will really be. You see, if it's one thing I've learned about this anime, it's that nothing is what it appears to be...