Perhaps they just needed to stay between their targets and the jumpgate, though no gate was shown on screen. If they guard the gate, then few of those ships would be going anywhere, they'd be sitting ducks. Except for the ones with jump engines, which are generally just the big warships. Also, they wouldn't need to get all their targets, the objective was to kill a few boatloads of refugees and crush their opponents' morale. If some get away, they can still achieve their objective, scare the hell out of people all over the galaxy.
As for the PPG, Sheridan might have had an unloaded one on him in plain sight, or one with a dead energy cap, knowing that it would be taken from him.
I have to say, I'm a little bummed that JMS is going to do a Superman comic. Does anyone else on here read his comics? I just don't think there's that much to work with in Superman. It's just a simple concept, which has been beaten to death. I still want more B5 comics, with all the wonderful complexity he could work with in that universe (again, I know). I just think he's going in the wrong direction with this. I still might read it though.
Raw Shark
"Be careful, Ambassador. Not every dream I've heard lately ends well for you."
Sinclair