It may be admirable to hold to non-harming principles even at the possible or even likely expense of your own health or life, but I'm skeptical about people who make such proclamations... unless, of course, they have actually faced serious life or death self-defense situations. I hear similarly grandiose statements from hardcore vegetarians that they would never eat an animal, even to survive.
I think these kinds of postures come from an idealistic place born of either a lack of imagination, or a life relatively free of real hardship. Ask someone who has come close to starving about the ethics of killing and eating an animal. Ask someone who lives in a war zone about the morality of causing harm in self-defense. If you've never been in these dire situations, it seems absurd to be presumptive about what others or even you would do when faced with such harsh difficulties.
On a more nuts and bolts level, I think it is wrong to assume that Aikido is about non-violence. O Sensei is not Gandhi. The 'harmony' talked about in Aikido is not about some kind of utopian, lovey-dovey world where no one gets hurt. I think the dynamics of Aikido are much more along the lines of 'what goes around comes around'. If someone attacks with extreme force and speed, that force and speed is quite likely to come back to them in proportion, as their face hits the ground, or a wall. In many situations, I can see the attacker coming to more harm than if you merely ducked and punched them a couple of times... imagine doing Ikkyo Ura on someone in a room full of heavy furniture with sharp corners... If someone comes in with a knife, that knife might well end up stuck in their own abdomen.
Another whole aspect of realistic Aikido self-defense is atemi. Many of the techniques and especially the pins have little hope of working against a strong, tense attacker without a fairly serious blow to a vulnerable point of their body. If that person is intent on serious harm, such atemi doesn't seem out of line at all, but if you don't use it, it is unlikely that you will end up in any position to show any mercy, and instead might end up begging for it.
Harmonizing is about doing what's appropriate to the situation, not imposing some fantasy or ideal on it. I see an ideal Aikidoka as giving an attacker what they need and precisely what they ask for. The more dangerous and out of balance their action, the more severe the reaction. Seagal dramatizes this pretty well (movie-style) when he shows reversals of attacks with shotguns, cleavers, etc...