I've had 2 ACL surgeries on the same knee(the second one was 100% my own fault).
I squat, on the regular. There is really not too much that relate between the two... unless you went dynamic with the situation. ACL holds your knee in place for lateral movement, and not so much static exercises.
If you do feel pain in your knee during squats, try elevating your heels. It helped me tremendously, in targeting the quad more, and taking pressure of the knees. However, I'm 6'2, so I think the relief from elevated stance is due to my heigh and not ligament status.