I have gammy knees, too, and while aikido made them worse for a while, after a few months it actually started to make them better. Obviously I dont know as much as you do about your injury or what your doctors have told you, but I can think of a few things that helped me out a lot.
1. Stretch - if you do stretches before class, you can do those at home too. Keep within your comfort range and do not push too far...your tissues will stretch rather than tear, and help keep you loose and limber.
2. Oneness Rhythm Exercises - only takes a few minutes, not stressful on your body, and a great way to improve your aikido if you cant go to class.
3. Ki Therapy - even if you can't extend too much ki yet, simply touching and pressing gently (no more pressure than if you were holding a pencil or piece of paper against your skin) around your kneecap, the muscles on either side of your knee, and the 2 soft "dimples" at each side of the bottom of your knee cap can help immensely. A few minutes each day should help
4. Seiza - Sitting in the seiza position will help strengthen the muscles of your knees and legs, taking some of the load away from the joint. No need to push it - just try to sit for as long as it is comfortable. This helped very much for my knees, but it may be no good for your condition, so if you do try it, play it by ear.
At the end of the day, whatever you're doing - if its hurting you, you should probably stop or slow down. Your body can take a lot more than you might think, just dont push him too far too fast
Its very possible that you hurt your knee in aikido. Aikido can be very hard on the knees, but that doesn't mean you have to stop - your sensei or senior students may have some ideas about how you can manage or strengthen your knees for training.