I have terrible knees -- was diagnosed with severe chondromalacia patellae in both knees 25 years ago, and with a minor ACL tear in the left knee 12 years ago -- and yet I never feel that clipping out exacerbates them. I think a worse scenario for someone with bad knees would be a clipless pedal system that A) didn't allow significant float during the full rotation of the cranks, and/or B) that locked your foot into a less-than-ideal angle relative to the knees. Compared to those scenarios, the ~15° turnout required to unclip seems like it shouldn't cause significant stress.
But da hell do I know? I'm not a doctor nor do I play one on TV.