Obama imposed the civilian average-Joe legal self-defense standard for use of deadly force on the military - deadly force only allowed if someone's life in "imminent" danger. So, of course, the captain's life was eventually in "imminent" danger under the circumstances, and they were ready to act when it was.
But at least he seems to have given them the authority to act on their discretion in using deadly force. That surprised me a little.
There have been two military crisis since Obama was inaugurated - this one and that thing about the surveillance ship off China. Both times Obama acted more forcefully than I'd expected, and in a manner that I'd expect the Joint Chiefs to recommend. It appears that he is listening to his military advisors and taking their advice. If so, it's one of the few hopeful signs I've seen out of his presidency.