Perhaps to ask the problem a bit more explicitly, I give you some random woman in yoga warrior pose:
Random women have always been a favorite part of my life, so I thank you.
If she wants to get the force out the front arm, and she is sourcing the back leg, and she is keeping her spine nice and straight by sinking the tailbone and raising the neck and all that stuff... if she were to push straight along that back leg into the spine, there'd be a lot of stress on the lower spine no matter what that had to be diffused somehow. How would you overcome that?
In this position the only thing it seems her back leg can effectively do, without leading to that stress, to get force out to that front arm is push asymmetrically on her torso to rotate it around that central axis of her spine, but the spine can not actually extend along that axis in that position. Whereas in the pictures of the baseball pitchers, the structure of their torsos are actually more directly behind the extension of the arm, so the torso can actually extend along into the arm.
Either way, the force seems like it has to travel roundabout, never straight. Is that not the case? Or would those breathing exercises enable the force to actually push straight zig-zags from foot to hip, from bottom of spine to top of spine, from shoulder to hand, without worrying about such stresses?
Well, here's several thoughts. First of all, many people are going to push from an extended back leg; if you look at the picture of the woman, for all practical purposes she has a "brace" effect, the same sort of effect that you could get by nailing a board in place of her back leg. If you go to a lot of Aikido dojo's, watch and see how many people actually work with their power coming from this straightened back-leg gimmick.
Secondly, some arts use an inclined torso to take effect of the back-leg in much the way you described (the Wu-style Taijiquan comes readily to mind as utilizing a lean for that purpose), so the idea of lining up the torso (as much as convenient) in order to maximize a back-leg push is already out there.
The point I'd make is that while mechanically a straightened back-leg brace is effective, it doesn't give you the options to respond in all directions instantaneously, so using the "Divine Intent", as Ueshiba termed it, to rig up force paths is more the way you'd want to do it in Aikido. Tohei emphasized the non-dependence on the back leg also by having push tests from all directions and by showing ki/kokyu demonstrations like this one:
Notice how the lined up back-leg is not a factor like it is with the yoga woman.
The breathing exercises allow for developing a structure that is not so dependent on local joint strength. I.e., it develops a strength where you need a strength, but it does *not* get rid of the need for some sort of strength to make the body a good framework through which forces can be conveyed... it's just a different kind of strength.
I'd note that in the picture above, while I'm sure the guy on one leg has some degree of the strength I'm talking about, he could also do the same trick utilizing various degrees of muscle, so I'm not saying that the above trick can only be done by a purist expert in the breath-developed skills.
And also... anyway you cut it, the ideal force is going to come from the ground to the hand so that the ground does most of the work, rather than the tightened joints and the stresses on the torso. In short, I agree that there are stresses, as you pointed out, but with good training you can dissipate those stresses over a larger area, thus lessening the stress at the joints.