Stunning enemies isn't usually an option for Link. Not to mention, out in Hyrule - a monster left alive is a monster that might hurt someone else later.

The Yiga were a bit different. They were human. But they were also always trying to kill Link, so he didn't feel so bad about them. The Sylphid were the same. They wanted to hollow Link out, leave him a shell for someone else.

So now they have a dead Sylphid, and they've got to deal with it. With a nod, Link starts dragging the body away from the door and towards the unmade cot. He shoves it underneath, and then shifts the messy sheets around until it can't be seen.