While all the advise so far is good, I don't think it goes far enough. If you're having pain for a couple of days after an Aikido class, then you ought to see a doctor!
Go ahead and modify your training, but also find out what's wrong.
While it might be the case that there is "something wrong" I can't say that I know that many adults who start aikido and don't have their knees,feet, and/or legs hurt after sitting in seiza for very long. The issue is that we aren't Japanese and didn't start sitting that way when we were young. I have heard that even the young Japanese students today are having the same problems as they no longer are customarily sitting that way all the time at home etc. It is my opinion that seiza isn't good for the knees. If you have a knee problem it is best to avoid sitting that way as mush as possible. I tell me students that they only need to sit in seiza when we bow in and bow out. If they have any discomfort they should sit crosslegged at all other times. It is quite possible for your knees to adjust. After over twenty years I can sit for prolongued periods without lasting effect but I definitely am stiff when I get up, more so as I approach the advanced years. Anyway, your knees have to last you. There is no real value to pushing it when it comes to seiza. If you're in your twenties I suspect that you'll get used to it. After that I wouldn't try to get used to it.