Nobody wants that. But please tell me what you think would happen, if a group of american soldiers encountered a unknown group of afghan people with firearms. They don´t understand each other due to language barrier, and even the culture is very different. Now the afghans point their weapons at the american soldiers - what would happen? That´s a rethorical question btw. Of course, the american soldiers would, at the very moment the afghans move their firearms, blow the unknown party to hell and back again. Unless we assume that japanese soldiers are trained completely differently, the same should have happened here with Itami´s group.
Again, nobody wants anybody to die - but no soldier would risk his life for such an unpredictable outcome. And it doesn´t make a soldier "evil" to shoot in such situation.
Of course, it was a group of hot lady knights and Itami had a boner, so ...