Two things have helped me with knee pain when I squat. The first was flax seed oil. I love that stuff. Second, take off your shoes when you squat, if you don't already. The heels in most shoes are slightly elevated, throwing your foot out of a natural alignment, and affecting everything above it.

I only suggest these if the pain is rather minor, cause if it's really a problem, you're correct, you don't want to injure yourself.