Not to be too flippant about it, but this reminds me of the old joke of the patient who goes to the doctor. While being examined, the patient moves his arms around and says, "Doctor, my arm hurts when I do this." The doctor turns to him and says, "Then don't do that."
I would say that if doing seiza hurts so much later, then don't sit that long in that position. Work your way up to it. If your teacher is talking away, then go ahead and change your sitting position to cross-legged.
I don't know of a single aikido teacher who has reprimanded anyone for having to change his or her sitting method. I'm sure that your teacher would rather have you with working knees, too. The best thing may be to let your teacher know about your condition and get his permission to sit out of seiza at times...