How do you know the ground-fire wasn't because the aircraft was obviously military? There are no reports of widespread fighting around Benghazi now. The indications are that it is fully under control of the opposition. The opposition would have no reason to fire upon evidently civilian aircraft, as reports suggest that they are doing everything they can to keep their economy and infrastructure running.
As I said earlier, it is excellent that the RAF are able to do this if it is genuinely militarily necessary. But if they are doing it for partly for publicity reasons for HMG (as Stopstart alludes), then they should be charging full commercial rates to the oil companies and paying landing fees to the locals, just like commercial operators do.