Originally posted by English:
Maybe he isn't.
It's all just speculation.
Keep in mind that he got a promotion to President of the 49ers about the same time that things started to become public about the blowup between the front office and Harbaugh. There were some reported conflicts between the FO and Harbaugh about the new stadium (locker room use on non-game days, sunny vs shady side of the field, not rescheduling practice to attend stadium event, etc). Marathe was clearly in charge of the stadium project.
Marathe also negotiates all contracts for the 49ers, not the general manager.
Does anyone doubt that Marathe, with his position as 49er president, with a history of steady moveup in the organization wields a high degree of power in the organization.
If his position was business only I would not have expected too much of a problem, but clearly he is not limited to that with his participation in several places to on field activities. Now considering Harbaughs focus on details and having developed his plans, and considering Marathes participation in a number of areas tied to analytics (review calls, on field guide, coach recruitment), it is not surprising that these two would come into major conflict. It is also not surprising that in such a conflict that York would side with Marathe. It also fits with the comments that Balke was not the instigator of the conflict, but was Harbaugh's last defender in the FO.
It is also interesting that many of the leaks established the conflict between Harbaugh and Balke. I would not expect any leaks orchestrated by Balke to say that, but would not be surprised in they were orchestrated by Marathe.