Naoto nods, and now that that is cleared up, she doesn't have any reason to stay. She wants to, a little bit, because this is one of the first ninja from Kumo that she's been able to actually talk to and she's quite curious now that he's proven not to be an active threat.

However, the situation is uncertain enough as it is, and Naoto does need to get back to her mission.

"Very well then; I will leave you to your exercises."

Waiting for an acknowledgement is only polite, of course. It will only take a second.