Although some reports this week have tried to downplay the rumors, there's been rumors nonetheless that there was a bit of a Lamar / coaching spat that was hitting a head. Now maybe they could have forced through that spat, but I'm picking the QB almost every time, but certainly for a 63 year old coach. If it was like McVay type I'd say hold on, but easy to chose Lamar over Harbaugh (and staff) if that was at all part of decision.
But yes, could still end up much worse than they were.