If he'd really just intended to take her out without proof, he could've shot her without engaging at all -- it would've been safer, if she'd actually been a witch. He had the gun out because he was ready for her to attack, and he might've have threatened her with it if the conversation had gone differently, but we've never seen them kill anyone in totally cold blood (without outside influences) and I don't think Dean was intending to start now? (at least that's how I read it, and how Sam did too, I think, or he would've questioned Dean a little harder...!)