If a move hurts, DON'T DO IT! When your body tells you something, listen to it! It's as simple as that. I tell myself I'M in charge of MY own health and well-being, so when a move doesn't work for me, I substitute or modify.
You can modify a move by taking out one of the elements. Take out the explosiveness of explosive lunges, and you've got static lunges. Take out the lunge aspect of the same move, and you've got another plyo move (plyo squats, for example, can be more knee friendly because there's less of a chance of the knee going out in front of the toes).