I seem to be in the minority here, but I'll play Devil's Advocate and side with the OP. Things in Libya have deteriorated to the point where the Embassy is suspending operations, clearly a sign for British nationals to GTFO. The Navy vessel sent to assist with this operation was, as the OP pointed out, barely armed (20mm, miniguns and GPMG according to t'interwebs). While it seems the crew of HMS Enterprise did a splendid job of getting British nationals and a few others out of Libya to Malta, I feel like the original question is valid: What if things had gone badly?
One reply asked the OP to 'please keep up' and posted a link to an article about the Tornado missions striking Libyan targets in 2011. Well that seems unfair. As a civilian I can only guess, but I bet my guess is good when I assume that those missions were planned well in advance with a lot of support. Quite different to the situation if Enterprise had run into hostile chappies with ill intent. Sure there are agreements in place within NATO to use bases for NEOs, but what if thing went down hill quickly, as they did for the US in Benghazi? A tooled up GR4 sitting at Marham does sweet FA for the people under fire on the way to the harbour, I'm sure.
Again, no disrespect to anyone, and thankfully things went off without a hitch, no matter why the British nationals were there and regardless of whether their employers should have evaced them earlier. But I bet everyone wold have felt better if the UK still had enough resources to have pointy things that make other things go bang a bit closer than East Anglia.