He willl kill anything he is capturing.
Also, I'm sure that everyone has noticed that the commander is easily distracted by enemies and often won't fire his d-gun. (It probably happens in XTA too, but i'm talking about AA). No, he wasn't outside the d-gun radius, he was just too busy trying to use his laser. Anyway if this is an AA only thing ignore it, but I think it's an engine thing.
