Best solution is to learn how to do a proper squat. Do bodyweight if you have to and work your way up by 1 pound at a time.
The only way you will injure your knees doing squats is either 1) doing it wrong or 2) overdoing squats. Conclusion from study: http://www.pubmedcentral.nih.gov/art...?artid=1322916
"The injuries typical of elite weightlifters are primarily overuse injuries, not traumatic injuries compromising joint integrity. These injury pattems and rates are similar to those reported for other sports and activities."
If you're doing your squats right, your knees will only get better, not worse.