This is one of the things that disturb me most when thinking about aikidō.
And other than historical, philosophical or techniqual question I don't have any clue how to ever get answer:
Why do people who deeply believe in pacifism practice a budō?
Why do people who do not want to hurt or injure another human being practice a martial art?
Why don't they learn one of the methods or ways that use and teach pacifistic ways to deal with aggressors or conflicts? There is so much to be learned if someone wants to. And it is really not an easy way to go. I myself think, it's much more chalenging than doing aikidō.
Basically; because it is one path. The central theme of Taoisme, Shinto, Boeddhisme, Confucianism is about your true self and its connection with reality, the world, the universe. One way of finding that true self and that connection is through meditation, but there are other ways as well; from going on a pilgrimage to practicing the arts. One of those arts is Budo or in this case more in particular Aikido.
How could this possibly disturb you so much?