Simply is not the right word. The bodies will be flying at them with high velocity and smack them in the face. In order to get inside the HK's have to jump, step, swing whatever - all those movements include detaching their magnetic boots, even just one. With nothing to hold onto the winds will push them back, they are simply too powerful. Even with a jetpack they wouldn't get in. They can't cancel the windows from closing if they are not inside. Its simply impossible.
What's to stop them from blowing up the panels that drop down to cover the destroyed windows? What's to stop them from destroying another group of windows and walking in after they've sent everyone into space by blowing up a few strategic windows?
Star Wars ships do not have the same Force Field Technology that is seen in Star Trek, not even in the New Republic era. While they are able to use forcefields for hanger bays, it appears that Force Field Technology is too bulky in Star Wars to deal with hull breeches, while you're looking at the Ravenger's hull breeches as an example of force field tech for Star Wars, I really doubt that was the case. In all honesty Ravenger shouldn't have even been flying, which speaks to how powerful Nihilus was, probably powerful enough to scare the heck out of Traya.
Not Jedi, biologicals. They are trained to kill biologicals, the Force puts a spanner in the works, there are no defenses that are specifically effective against Force users. They have an edge in just about anything. E.g. bomb explosions they can shield against, same with flamethrowers and carbonite attacks, they can push toxins out of their bodies, they can deflect turret fire etc. And sure, they have a factory, but I don't think production is anywhere near that fast. Eventually, superior numbers will prevail. Let's also remember that if the invasion of Malachor fails he lost what, 100 units? And has 0 time to build more.
If you actually see the droid production facilities of the HK Factory, they easily have hundreds if not thousands of droids near completion in massive assembly lines. You can see it in the background. Losing 100 droids wouldn't be that big of a deal... Additionally, if Traya loses her fleet, she wouldn't have the ability to conduct an invasion of the droid factory anyways.
Btw, the Sith Assassins in KotOR II were not exactly Galen Marek, the Exile, Revan, or Luke Skywalker... Some of them actually died from gas mines in TSL if you lure them into them. The Sith Assassins also got stronger, the stronger in the force their opponent was. Considering HK units aren't force sensitive, that also seriously limits the power of these assassins.
The factory will have to shut down if under siege. They'll only have whatever supplies are on hand, enough to make a few more droids, but not very many. And the Sith don't need to force their way into the factory, just bomb the entrance and cave in the base on top of it.
The military facility above the factory survived a full-scale orbital bombardment already, and the actually HK factory, is beneath another facility that is beneath the military facility...
Additionally, it stands to reason the HK-units would have tunnelling equipment to dig themselves out if someone tried what you're suggesting (they were psychotic, not complete idiots).