Squatting actually helped me recover the normal use of my leg. I tore my ACL 10 years ago and suffered a failed autograft surgery where the surgeon cut out the middle 1/3 of my patella tendon and used that as the acl replacement.

 The surgery failed and my knee cap shifted out-of-place because of the cut petella tendon. After 10 years, I was suffering from patellar tendonitis. My involved leg was much weaker and had a drastically reduced range of motion which caused a poor gait and all kinds of foot and hip pain.

The surgeon told me to never squat, but I figured that my leg was so messed up anyway after 10 years I might as well try it. Well, the more I squatted the better the leg got. I started out with light weights for high reps to get the range of motion back. As soon as the range of motion returned, I started ATG front squatting and then slowly adding weight on the back squats.

Now, 3 years later, I just PRed 605 pounds on the back squat and 455 on the front squat. I also deadlift without any problems. I tried olympic cleaning for a couple of months, but that caused my knee to swell. That's my experience any way: squat and deadlift without an ACL, but don't do Olympic lifts. Two tips that helped me were:

1. keep all the weight on my heels at all times
2. squat very frequently, every day if possible and at least every other day.

That really seamed to maintain the range of motion and keep the stroke efficient and safe so that when I fail on a set it's because my hams/glutes are spent and not because I'm shifting my weight oddly to baby my involved leg.