Khan's expression clearly suggests he doubts that statement very much, but he's already made his decision. Doctor Bashir is either foolish or ethical enough to offer his help without deceit, and that's something he hasn't experiences in a long time - three hundred years, even.

He offers Julian a shallow nod of assent, but distinctly makes no promises. Given that he has no idea who is on this ship or how they might react to him, he reserves his right to defend himself by any means necessary. For now, he'll tentatively trusting Julian's judgement.