I'm not sure how that's a conspiracy theory. Those are the facts that have been reported by numerous gaming news outlets.
2K had no plans of making 2K13 and MLB didn't realize until very late that there would be no MLB title on XBox, so MLB threw them a last minute deal to give it a spit and polish for 2013 as no one else would be capable of putting out any product for 2013 on such short notice.