Link listens closely. Takes a moment to gather his thoughts, figure out what to say. Though he starts by shaking his head in agreement with Atom.

No, Atom can't afford to hesitate. Hesitation means death or injury. For himself, or for someone else.

"...I kill their soldiers because they hurt people," he says. It's blunt, but it's the truth. "They die, or someone else does."

And in the end, Link preferred that they died. In fact, it was his duty as a knight. It was his job to do the dirty work, to get his hands bloody.