It was his defense weapon. He got caught without it.
Seriously though, I think he has some past with the vorts. They didn't seem to speak to him, and he gave a reply. Maybe he had a feeling this would happen?
Thats not even worth thinking about, it just won't happen. The vortigaunts seemed to be holding him captive in that crazy border-like world, and due to that he couldn't follow you around city 17.
Valve said you come out of stasis earlier than Gman wanted, and the vortigaunts saved alyx (some prayer causing her to teleport or something?). So with Gman trapped, you come out of stasis and are put with alyx to save her it seems apparent to me. So you fight to get her out of the city, probably because she is special, or she must be kept alive for some purpose. Gman wanted her to die(he saved you but not her, vorties did that!), which is why he's pissed...thats how i see it. God knows whats going to happen to him now.