Don't twist your knee
I came to Aikido with a history of problems with my knees. My problems stem from imperfect structure of knee cap, but I think the advice I got is important to everyone:
Keep your knee above and in the same line as your foot.
When turning, don't pivot your foot in the mat: first change the direction of your foot and only then move so that your knee is never twisted.
I dont think seiza by itself is bad, though suwari-waza may be; I try to avoid it when I feel I start to feel pain, as it puts much pressure and twisting on the joint and knee-cap.
I also suggest you discuss this with a physiotherapist. He/she may point out to you the source of your problem and maybe a way to avoid further damage. Don't just stop all activity.
I'll think of more,