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.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.
The HK's could simply push the bodies away and move through them with the magnetic boots. Then stand on the ceiling until the shields go down. Or cancel the shields from even coming back online with the console.
With the invasion the HK's are programmed to kill Jedi, and the defenses of the factory are programmed to also kill Jedi. The Sith would be slaughtered. the HK's could also use flamethrowers and carbonite attacks to kill the Sith. Or they could be suicide bombers and run with bombs about to go. Droids can be programmed to do anything.
EDIT: with the factory, new droids are constantly being produced. The numbers argument is sort of, not completely, but sort of invalid.