Also, I'm betting this was just the last straw with BBC, not the first offense. In the show, Jeremy would constantly make reference to the fact that he was doing things his way and not how producers wanted him to do it... which likely was not always the joke people thought it was. The irreverence to the BBC and its producers was a big part of the show's popularity, but was probably also a thorn in the BBC's side. I await more Stigs driving tanks in protest but don't think it will matter.
tldr; Jeremy kept pissing off BBC so they're probably happy to be rid of him, ratings be damned. We'll all miss him.