I think there's Bad Blood between ownership and ANYTHING & EVERYTHING related to Ditka and his 'tree', in whatever manner. imo...that would be an admission to being wrong about knowing how to do things better than Ditka. Ditka and Harbaugh are not far apart in coaching personalities. Its their way or 'the highway.'
I happen to be of the opinion that sometimes the whole is greater than the sum. The players of that era will all say it was Buddy Ryan's defense, and will be all in for Buddy over Ditka. However, Buddy Ryan didn't exactly light the world on fire as a head coach after he left.
I think it was the combination of Buddy and Ditka that made that defense great. In some ways, the same thing happened with Lovie Smith and Ron Rivera. Ron saw the flaws in the vanilla cover 2 that Lovie liked to run, and adjusted the defense to a hybrid that Lovie couldn't stand, even thought it was more effective, because Lovie's ego wouldn't allow for him to have someone to improve "his" defense.
The NFL coaching ranks is so filled with Ego, and yet, Ego is what ends up fucking everything up more times than not.
You need an ego to get good enough to be in the NFL, but you need to know how to temper and direct it in order to stay and stay successfully in the NFL.
Could argue that ego is the reason Harbaugh is no longer in the NFL despite his track record - he never learned to control his own ego.