Like most similar things, I doubt we, the plebes, will ever know the full truth of the matter. In general, you don't see many people going off in detail about why they were fired from a job, because for one if you can't prove everything you say, you can get sued, and what's more the policies at many companies involve some degree of non-disclosure agreement, or at least have internal policies that make gathering proof of wrongdoing or a dispute themselves an offense that can get you fired. In most companies if you say record your boss lying to you, you violate an agreement not to use recording devices, and thus gave them cause to terminate you right there. It can be a huge mess. On top of all of this, a huge mudslinging match with a former employer tends to make it so nobody else wants to hire you, no matter how right you might be... As sharp tongued as Jim might be, he does apparently want to keep working in and around the industry, or at least the media portion of it, so I'd imagine even if this was really ugly, this is the kind of parting we'd see anyway simply out of a sense of professionalism.
*THAT* said, if I had to make guesses as to why Jim was let go, well I'd point out that he promotes himself as a "gun for hire", and seems to produce a decent amount of material. It wouldn't surprise me if Destructoid had some concerns about the extent of his activities, even Jim himself points out he can't focus on doing all of this other stuff and being a full time editor for them. Not to mention that Destructoid seems to be trying to promote itself as a highly professional, and dare I say "classy" site. Jim is a guy who just did a video here where he humped a blow up doll, that kind of thing doesn't exist in a state of limbo all by itself, everyone who associates with Jim has what he does in all of his material reflect on them to some extent. Jim's style of humor is great, but honestly if I was running Destructoid and had the intention that they seem to (keeping the irreverence within limits) that might render me concerned as well. Add to this that Jim continues a crusade against Gearbox, which while righteous, can be a touchy subject given the sheer amount of popularity that company has due to it's success with "Borderlands", it still moves decent amounts of content, and has a fanbase that seems pretty fanatical and to have already forgotten about "Aliens: Colonial Marines" for the most part. While not the kind of immediate backlash that hit Gerstmann over "Kane And Lynch" it wouldn't surprise me if Jim's crusade against Gearbox caught up with him, or at least contributed to this. Being RIGHT is sadly not what's always important... and again, the guy is "parting ways" with his previous employer shortly after humping a blow up doll which had a product from that company taped to it's face as the punchline.
At any rate, I wish Jim well, and hope he continues to be on The Escapist for a long time to come. He makes me laugh which is very important at this stage in my life... while also making some great points even if I frequently disagree with him in his overall conclusions.
I'm half asleep so hopefully this is all coherent. In short, I doubt we'll ever know what happened for a number of reasons, and I personally suspect that if he was "asked to leave" (or told to change or leave) his blow doll humping probably had more to do with it than backlash to a game review. I mean honestly, it was great, and hilarious, but it was kind of over the top and not everyone is going to want to be professionally associated with something like that no matter whose site it's on.