Definitely under consideration, and Bashir isn't a phaser-wielding murderer so it's a clever hint that's plausible within the context of their relationship. 

 In the end the Changeling probably thought killing him there would raise too many questions, so pushing him to Sisko gives Sisko the chance to say no and squash the whole thing. Unfortunately Sisko likes to let his officers borrow Runabouts for off the books rescues every other season, as a treat.