A few incoherent thoughts:
I actually find this issue one of the most confusing in aikido. Take throws for instance, even the softest throws if applied on an untrained person and on a hard surface would cause substantial damage, much more than the strongest atemi to the face.
The barrier between violent or not, damaging or not, painful or not is thus blurred.
I myself am not a natural striker, I have a dislike for atemi, and avoid using it in training despite the risk of offending my teachers.
I think training should as painless and as peaceful as possible, but without sacrificing the intensity. However, it is an illusion for anyone who thinks that he can control the amount of violence in a self-defense encounter.