Well all the studies I have seen state that it isn't worse, and quite a few that deep squatting will do nothing but strengthen the ligaments in the knee.
Also, with going deeper as opposed to stopping at 90, isn't alot of the load transferred from the knee to the hips? This would be my main reason for thinking deep squatting is better.
So long as you aren't free falling and bouncing out of the hole, deep squats should be fine.
Also you are right about injuries and other factors effecting it.