Stupid plot disagreeing with the OP and my analysis/predictions. They may be on the same side but there's a still a chance the new and the old will end up having it out over something, wouldn't be the first time Gundam pilots ended up fighting against their original 'side'.

As to the Sumeragi being dumb, the only smart thing to do in that situation would have been to not go. They already knew it was a giant trap even without the lovestruck nerds plans, but they went anyway because stopping terrorists is part of what they do. Sumeragi apparently came up with several plans and contingencies to try and get them out, however when it's 4 vs 864 there isn't really viable solution because no matter where they might have gone the enemy could just throw more bodies at them to keep them pinned down.

I really didn't like the way the time kept skipping forward from an action standpoint, but it did a good job of showing things from a dramatic standpoint. Sumeragi and the rest of the crew weren't involved or keeping appraised of the situation at all, they were simply waiting for the meisters to make it out somwhow. Considering the amount of caring some of the crew have shown for particular meisters I am forced to conclude they were doing nothing because there was simply nothing they could do to help them but wait.

One thing that really bothers me though is Allelujah, why do they continue to use him knowing that one the people he might encounter on the battlefield can completely incapacitate him just by being nearby, now that's foolishness IMO.