I've been training for 2.5 years now, having knee problems for 2 years.
Actually I hurt one knee in a seminar while working with someone I didn't know. There were so many people on the mat that the sensei decided on one technique NOT to throw back but only take out of balance. So my partner did throw me and as not to hurt those behind me, I jammed my knee into the tatemi...
The other knee got hurt half a year later in quite the same manner.
They healed by themselves, in about 4 monthes (knees take time) and I didn't take any medication or knee protectors.
For a different reason (nothing to do with aikido at all) I got an inflammation half a year ago, and have been practising with knee protectors ever since.
If one trains right, knee problems should not occur. You might like to train more on walking correctly on your knees (a few minutes before or after class) it will show great results in the long run. Have your teacher correct your walk (you should not throw down your knee on the mat but more slide it down. it takes alot of training to get it good). Also work on your rolls, so you don't land on your knees.
I'm not sure if you wear out your knees in aikido. Maybe aikido has more techniques on knees than other MA (but I don't know).
Still, if you are careful and workout correctly, I don't think you need to get hurt.
There are people in our dojo training for longer years than me and they have no knee problems.
Anat