We will never know the true story but one thing that does have some legs is the fact that Harbaugh and Baalke certainly appear to have been on different planets on the 2012 draft. Baalke drafted some small quick guys at the top of the draft to give the offense much needed speed and Harbaugh virtually ignored them. That makes Baalke and the team look bad.
We have ranted about the lack of development of WRs and the offense in general for months now. No matter how one views this trade story, there has to be some friction in the FO over the lack of offense. So while there is likely to always be some friction between a HC and a GM, especially when the GM has final say over the roster, the offense, or lack thereof, would lend some background to developing such a story.
Friction between Harbaugh and Baalke may have something to do with the failure to get an extension done so far. Harbaugh MAY be asking for final say on the roster and Baalke is resisting. So if that were the case, and such a thing could easily have leaked, then a phone call from the Browns might have happened.