Dubas was fired for an attempted power-grab from the man who gave him his NHL life on the basis of his (Shanahan's) faith in him (Dubas). The week that was Dubas' undoing and the relay of events, has to my knowledge, never been corrected by Dubas. And that speaks volumes in terms of his culpability.
"More autonomy" was leveraged publicly and in bad faith. That additional autonomy that you've cited, was part of Shanahan's role.
Dubas' definition of "more autonomy" included ignoring Shanahan's collegial advice, all but rejecting the once agreed upon contract, ignored repeated requests to talk and confirm said accepted contract, and then renegotiate through his agent...ONLY...to realize the mistakes that are red flags in any like situation.
The best thing Shanahan has done so far was bring in a new culture of winning to the point that constant 100-point seasons bore us, which not incidentally, included our organization's first Calder Cup. The next best thing after all of that -- which included getting best of the best management, including the shock of nabbing LL (and don't for a moment pretend like you didn't grow ten feet tall when you heard the news on the day) -- was righting another wrong, that he apparently didn't notice before.
But when he saw Dubas in a way that few of us did or could, he didn't puppet master a single minute. Not through back channels, not through text or email or phone. Nah. Shanahan took 24 hours from point of realization, let it all sink in, then drove to tell Dubas in person that he was done.
Where this notion that Shanahan is duplicitous or deceptive as a manager is beyond my ability to suspend disbelief.
He can't make our forwards grittier, take less money, score series winning goals or save soft series ending ones. He has to guide the club in modes of high-regular season achievement, and high post-season disappointment with the pieces we have and attempt to maintain the former just to have a chance at the latter.
Where better options exist, they are few and far between and not compelled to sign in Toronto. If he was a puppet master of any repute, then he would have signed our Big 3 to graduating contracts rather than publicly appeal to their (apparent?) sense of championship aspirations and personal sacrifice. But he's not, and he did.
It was Dubas who tried his hand at manipulation. The once rumoured and denied position with Pittsburgh was eventually taken when Dubas' agent couldn't use it as leverage in for a piece of Shanahan's seat.
If anything, Shanahan used his position to insulate Dubas. And when Dubas turned on him and asked for the very shield that cultivated his entire professional career that but for Shanahan's faith would have never happened, Shanahan remembered that a shield is also a weapon when needed.