He recommended to the First Officer that they retreat from the planet and she gave him an order not to do that. She went to sick bay after but I don’t think command was formally transferred to him.
So he looked for an alternative that would keep them safe while still executing a superior officer’s instructions, and he got it wrong by misunderstanding compounds in the debris that he’d never encountered before. If he’d been right about the debris it would have been a genius move. As it was, he followed orders and looked for non-suicidal way to do that.