Oh gosh, it's been so long since I've played... I know there were some sort of targets (lights or generators or somesuch) up on the walls and IIRC, you had to deploy a medium-sized mech into sniper-turret mode in order to shoot those, instead of the missile itself? (small mechs deployed as the machinegun turret might have also worked)
I think there might have been a part, after you do all of that, where you have to pick up an Anti-Air Missile and use that on one of the big missiles as it's firing out?
It's hard being the voice of reason when you're surrounded by unreasonable people.