There's enough corroborating evidence that I'm willing to bet Konami did something stupid.
On the flip side, Kojima is notorious for trolling fans and drumming up controversy. However, I'll keep working under the assumption that Konami did fire Kojima (despite their wording to make it seem like a mutual deal). Kojima will be fine with whichever company manages to snipe him, he's a brand name now and has been one of the most influential (I'd argue the most, but that's not here or now) people involved with gaming in the past 18 years.