I've tried just about everything, including the patch, and I was still getting the error quite frequently, but I've discovered two things:
1. It occurred more often for the levels where you kill a lot of enemies, when they keep respawning, so a stealthy approach is definitely a good idea.
2. I think it has something to do with the glitchy graphics thing, which can be fixed by alt+tabbing out of the game and then getting back to it; so if you do this every time after you load / quick load a game, the error should be gone. I'm not 100% sure, because I didn't test it it on a very long period of time, I was almost done with the game when I discovered it, but it did work every time.
I hope this helps, good luck.