The US, UK and France formally agreed to pass command for the military operation in Libya over to NATO, but substantial questions remained about the changeover.

Under the terms of the deal, NATO would manage the no-fly zone, while political oversight of the mission would be outsourced to a separate body made up of members of the coalition, including Qatar and the UAE. But I don’t think this gets the US out of the lead role, necessarily. NATO member states will still command the mission. In fact, US supreme allied commander in Europe, Admiral James Stavridis, would be the likely candidate to run it. Furthermore, all 28 NATO members would have to agree to take command, and that degree of unanimity does not yet exist. In particular, Turkey, the third-largest NATO member and only Muslim nation in the alliance, seems wary, though they could perhaps come around.

But larger questions about the mission began to appear, with members of the coalition appearing to go well beyond the boundaries set by UN Resolution 1973. The British attack on one of Gadhafi’s residences on Monday continued to cause a rift between 10 Downing Street and the British military, who squabbled over whether Gadhafi himself was a legitimate target. And this story of Marines rescuing the pilot and weapons officer from that downed plane near Benghazi could spark a new round of outrage:

A Marine Corps officer said that the grounded pilot, who was in contact with rescue crews in the air, asked for bombs to be dropped as a precaution before the crews landed to pick him up. “My understanding is he asked for the ordnance to be delivered between where he was located and where he saw people coming toward him,” the officer said, adding that the pilot evidently made the request “to keep what he thought was a force closing in on him from closing in on him.”

In response, two Harrier attack jets that were part of the rescue team dropped two 500-pound bombs before a Marine Osprey helicopter landed to pick up the pilot, at about 1:30 a.m. Tuesday local time. The Marine officer said he did not know if the people approaching the pilot were friendly or hostile or what damage the bombs had caused.

Channel 4 News in Britain reported that six villagers were shot by American troops in rescuing one of the two airmen. None of the villagers — who were interviewed by a reporter in a nearby hospital — were killed, although a small boy may need to have a leg amputated.

“No shots were fired,” said Capt. Richard Ulsh, a Marine spokesman aboard the Kearsarge. “The Osprey is not armed, and the Marines barely got off the aircraft. I was in the landing center the whole time, where we were monitoring what was going on, and firing was never reported.”

The military is investigating, and we don’t know yet where the truth lies. But if you can shoehorn that into the “responsibility to protect” doctrine, best of luck to you.

It’s entirely possible, and my best hope, that this ends up going well. The fact that anti-Gadhafi voices have come up from the underground in Tripoli is a good sign. But Gadhafi himself shows no sign of giving up, and that means a possible stalemate, with the disorganized rebels unable to capitalize on air superiority and Gadhafi’s forces dug into the major cities. And while the theory is that no shots will be fired in anger by foreign troops on Libyan soil, that pledge may have already been broken.