I can relate SOMEWHAT to how you feel, BUT, if you are using aikido in the way it was originally conceived then you should cast your guilt aside.
One of my most favorite quotes:
Shioda Sensei once said, ". . .after the demise of the samurai class, the martial "arts" became martial "ways," and great value was placed upon them as a means of generating the moral strength necessary to build a sound society. Nevertheless, in the last analysis the martial arts are the arts of fighting [women and men]--of the samurai--and if the basic objective of defeating the enemy is lost sight of, then as martial arts they must cease to exist. Accordingly, they must not become mere intellectual exercises, the fundamental budo "conduct" must not be treated lightly and the "way of technique" must not be neglected as a form of spiritual and physical training."
So I believe that you either practice, and use the martial ways properly--and come out the other side of a violent confrontation as properly handling it--or you die or become maimed or injured. It's up to you. That's why I practice my style of aikido, for life or death situations. If someone tries to hurt or kill me. . . I don't feel bad about breaking their bones or sending them to the hospital. It was their decision and they picked the wrong person to mess with. This is true self defense and true budo. Hell, if they survive, they might even learn something. It might change their life around.
At least in my style, aikido is the ultimate self defense. The teaching methods haven't changed much for a long time (in my style anyways). That's why we practice a technique literally 100's or 1000's of times--so it stays fresh in the "muscle-memory".
hope my 2 cents helps.