I thought Kotomine was quite taken aback by Kiritsugu's wish when he heard it from Irisviel? As in, 'What the hell is this idiot even thinking?'. IIRC, he said something about war and strife being fundamental to human nature so wishing them away would mean drastically changing humans themselves? And that was something Kotomine himself couldn't accept? Am not certain though, would need to research once again.