I don't mean to terse with you, Beni, but you're being a bit of a stubborn idiot when it comes to the HK assault team. Yes, their anti-stealth technology will surprise the Assassins... if the assassins confront the HKs alone, and the HKs are able to deploy the technology. But this assumes the HKs will not already be in the chaos of battle, etc. And honestly, the assassins are really more of a deterrent against organic targets.
Now, as for the scenario it seems you're envisioning. When I say "turret" I don't mean an automated blaster on a swivel mount. I mean a mounted assault cannon in a fixed position, sighted on the established kill zone, manned by a veteran Sith trooper. The Sith will not "pour into the room" to be massacred by the HKs. Quite the opposite. They'll be waiting and dug in, and will tear the droids to pieces. HKs are unshielded, and ion weapons would be standard issue for many Sith troopers, especially since its known that their enemy is a droid who employs other droids.
You've conveniently ignored any of the numerous strategies that could be used by Traya's forces to undermine the precious technological marvels that G0-T0 will purchase. The Sith troops under her command include numerous veterans of the Mandalorian Wars and Jedi Civil War, people like Atton Rand and Azkul, who are ruthless and superbly trained. They have good armor, personal energy shields, and powerful weapons, as well as the advantages of defending a prepared position at numerous chokepoints. They will be supported by stealthed assassins and Sith Lords, who can use numerous Force powers to augment the firepower they already bring to bear, and if the fighting gets into close quarters they'll have the edge over the HKs because most if not all Sith Troopers are trained and equipped with vibroswords and other melee weapons.
As for the ships getting yanked out of hyperspace, I doubt they'll get off with only losing one or two craft. The Sith will bombard them with missiles, since they only have to worry about firing one volley before they lose their targeting information. Once locked, the missiles can't be shaken with the stealth fields, and the sheer volume of warheads will likely overwhelm whatever countermeasures G0-T0 happens to have equipped them with (which will be nothing out of the ordinary since he expects this to be a stealth mission and most of the space will go to fuel/ammo/HKs)
And even in the best of circumstances, I don't think you can activate your cloaking device before coming out of hyperspace. Those two systems, individually, seem to draw down the buik of a vessel's energy output. (especially a small craft which is probably already pushing the limits of its power plant by having a cloaking device).
As for the HK production plant, we're putting an awful lot of stock into a few background images that originated as cut content from a game. So it's a very loose interpretation of canon to even consider the factory in the first place. If it was cranking out hundreds of droids, G0-T0 wouldn't have had to send them at the Exile in small groups. The same goes for assuming that the MSG is inaccessible simply because you don't see a console for it in the rushed, choppy ending of KotOR II. I would say, if the device can be reactivated, it must be accessible. Now, you would certainly need the engineer who designed it if you wanted to carefully recalibrate and fire the weapon again, but if you want to destroy it? Just send some demolitions teams.
And if its very hard to find.... well how will Bao-Dur know where it is? It's not like he's visited the planet since it was crushed and reconfigured. To be honest, I'm not really sure why we're allowing the MSG, since it's become nothing more than an irritation at this point, and there's almost no concrete information on what it is and how it works. Will it work if moved to another planet? Maybe, but Malachor had some special gravitational thing going on that made it possible, so I guess it's only usable there. Is it buried underground? Not sure about that either. Well, could someone destroy it since it's basically a time bomb right next to their headquarters? Oh gosh, maybe it's super hard to reach, and so they can't sabotage it.
If the MSG cannot be deactivated, then it only makes sense, strategically, for Traya's forces to lay a series of elaborate traps around it and have a Quick Reaction Force standing by to swoop in and pummel the force sent to mess around with it. Then prepare the Academy's defenses and slaughter whoever attacks the Academy, while having shuttles prepared to evacuate and regroup with the fleet before heading off to somewhere else (NOT Korriban, it's so obvious it hurts) if it looks like G0-T0's troops might be able to activate the MSG after all.