If you really wanted to survey the risk, it would be useful to distinguish between chronic and acute injury risks.
I think most acute injury risks are avoidable or bad luck. The way to protect yourself against these is to keep on the alert for uke-uke collisions, and avoid getting out of your depth - which could take the form of jumping into practice too intense for you, or training with people who are reckless or abusive. There is no reason to volunteer for participation in either scenario, unless you just want to take the risk. Sometimes, though, accidents happen, and that's just life.
When it comes to chronic injury, I think suwari waza/hanmi handachi (sp?) is the most inherently damaging part of Aikido. Knees just aren't made for that kind of activity - too much twisting/torque on a joint that is basically a uniplanar hinge joint.
In general, I think the way to avoid chronic injuries is a sound, basic weight training regimen that focuses on the big compound and bodyweight movements. Proper resistance training develops radically increased strength and injury resistance in bones, tendons, ligaments, cartilage, and of course, muscles. It doesn't make you invincible, but you might be looking at a durability increase of 2 or 3x, which is nothing to sneeze at.