Either you guys really suck at developing HK-47 or you're playing with some hardcore difficulty-adjusting mods. I find the HK Factory level easy while playing at highest difficulty. After I find the Capacitator Armor, I find it very easy indeed.
Here's what I make sure I have on HK:
- Agrinium armor (until I find Capacitator)
- Two good pistols: Mandalorian Rippers or ideally Disintegrators, if those dropped
- all 3 two-handed combat feats, to use the pistols without penalty
- for both pistols, best possible upgrades of the following line: Mandalorian Chamber, Rylith power cell, Accuracy scope
- Master Sniper Shot (with rippers/disintegrators you can get a high % of critical hits)
- A lot of Construction Kits for self-repair, and some points spent into Repair to make these more effective
- equipment that increases Dex or Con.
With all that, the Factory is a breeze. No point in activating shields in the middle of a fight, as the Agrinium armor means your own hitpoints absorb damage better than a shield would, so it's better to just self-repair as needed.
Note that the above is not the only possible good setup. Also it's not even optimised for the factory, wher eyou only fight droids - I'm sure I could get better anti-droid damage if I used some ion upgrades. The setup I described is good all-around, against all sorts of targets.