Re: Non-Harmful Techniques
I think the questions you're asking are fundamental to aikido. We should, in fact, ruthlessly examine our teachings to see if they are consistent. Principles and technique must exhibit true integrity (not just the "martial" integrity you mention).
A lot of confusion arises because, as you say, many of our techniques would hurt an unskilled (at falling, anyway) attacker. What is not emphasized enough is that to throw someone successfully is an attack, not a defense. This is ok, because just as we need to know how to defend from punches, kicks, and grabs, we must know how to deal with being thrown. But just remember that it is not the defender who does the throwing -- it's that the original defender has become the present attacker. This convention makes for efficient training.
But there should also be times where we specifically focus on techniques of loving protection, where we assume the partner cannot be responsible for how they fall. In such cases, throwing is not an appropriate response. Almost all techniques can be done in such a way as to bring a person close, and then lead them in a controlled manner to the ground, where they may be pinned. The late R. Kobayashi emphasized this in all techniques, and it was shown how to hold your partner so that they had no possibility of hitting their head on the ground.
It can be done. It must be done, as you have pointed out there are many situations where hurting the assailant would be competely counter to our defensive aim. This is a purely pragmatic thing, and need not even be driven by "lofty ideals."
You are not alone in seeking out this particular approach to aikido. I would be happy to discuss the matter in more detail, should you want to contact me directly.