I think that's the rub. Injuries come from catastrophic, unexpected / unintended events, such as landing an otherwise perfect breakfall on top of a fellow student who happened to occupy your space a split second before you arrived there, or any of a number of zigs that should have been zags when practicing randori at or near full-speed. There are numerous opportunities for this in Aikido.......

So I wouldn't worry about the breakfalls just because some folks blame bad backs on them. I also wouldn't worry about suwariwaza because some folks blame shot knees on it. I'd worry about whether or not the student takes the time to warm up, stretch, and listen to their body tell them whether they are doing something right or wrong.