Wait, wait wait. Big problem I just realised with this plan. If the droids explode the windows, all the air suddenly rushes out, so fast and so powerfully that everyone inside gets sucked out. So how on earth are the HK's going to get in when air is blowing them in the opposite direction and bodies are flying into their faces? Sure, wait until all the air gets out, but no because once that happens the windows seal. Leaving the droids awkwardly floating off into the distance like Team Rocket, then getting blasted apart by fighters.
Yet the position of the windows are right near ALL personal on the bridge. Quite possible with the right timing and positioning.
This would be after Malachor, and under the assumption the attack would fail. Just another one of the possibilities. I think the factory would fall, yes it would take time but Traya has an advantage that G0-T0 does not, numbers. She can just keep pumping Sith, assassins, droids and troopers into the place until she wins. HK droids are tough, but how long can they last against lightsabers, lightning, ion weapons, grenades etc? And concerning breath control, only Traya. But those gas vents can simply be shot at/avoided.
With Bao-Dur, how will Traya learn of the factory before the invasion of Malachor? That's is the only time that HK's will be really attacking- well the ships and the protocol droids but still. I also beg to differ that the factory will fall. With no breath control(yes, no? whats the verdict?) and many, many defenses I don't see the factory falling. Especially if G0-T0 gets the fleet. Orbital bombardment anyone? The factory has survived it before. Those who besiege it though will not be so lucky.