I think we should differentiate between two types of difficulty here. There's "difficult" in the sense that enemies hae attacks that do an incredible amount of damage to your party, and that will most likely result in the death of many if not all of your team. Here, reloading and reloading and reloading a save is to be expected. Notice how this doesn't touch upon how much HP the attacker has, only how strong his attacks are.
The second definition of "difficulty" is opposite: enemies have a high number of HP, but their attacks do a normal to negligible amount of damage. Here, there's a very minute chance that you and your party will die and have to reload a save; the defeat of your enemies are inevitable, so there's no impetus to fret about your party, since there's no real danger.
The HK Factory would fall under the latter definition of difficulty. Enemies have high numbers of HP, but HK-47 has an even higher level than them, so there's no way in which he can die. The only problem to this scenario is that it takes bloody forever; everything seems like a chore, and you eventually want to be done with the whole thing. Frankly, it's worse than Malachor's grind, because at least there everyone died after three or so lightsaber attacks.
I actually really enjoyed Nar Shaddaa after T3 got the transponder codes, and Atton, T3, and Mira had to run to Akkere. Why? It was difficult, in the first sense. My finger was on the F9 key, having to quick load every minute. But you know what? It was fun; it was a challenge that I knew that I could win, I just had to change my tactics and find something that worked. If anything, I want the HK Factory to be challenging, but like the Nar Shaddaa NPC-only section.