Gibraltar
I wouldn't believe all you read in the papers or online media. About the most reliable is the BBC but they are very good at purporting to have an impartial take on matters.
As for armed escorts, all security services in Spain are armed, including your shopping centre "mall cops". The Guardia Civil fulfil the role of the coast guard, and given the long history of naval "spats" between the two countries, why not have an escort in to and out of the waters. I'm not saying the incursion was legal under the laws of the sea as it clearly was not but an incursion by warship and a scientific vessel are two very different matters. I'm just suggesting we don't get all "American" and gung-ho about it.