Yes, there was shite off the field. But Rafa made mistakes in not using it for the benefit of the team.
And even if he tried, there were just as many supporters willing to use the occasion to stick the knife into Benitez. It was commonly thought that Rafa had instigated the mess and there were a lot of supporters for Gillett and Hicks at the time. There was much reservation about the march support of Rafa, there was willingness to understand the Klinsmann fiasco because it was assumed Rafa brought it on himself, there were the infamous threads calling in support of Rafa or those suggesting other managers, some even thought he deserved it given the Newcastle press conference, and a lot of people still remembered his demeanour after Athens. I think given the lack of information people had at the time to the state of relationship between Gillett and Hicks, Rafa was put in a hard place and almost had no bargaining power. So how was he supposed to rally the supporters for the team, when his own position was so weak?
Now his position is diametrically opposite; it is so much stronger because the rift between Gillett and Hicks has been revealed fully. Those that supported Rafa at the time of the Newcastle press conference did as much on the basis of intuition and faith in the manager and trust in those few members who had some access to behind the scenes knowledge. I know because I was one, and it was a difficult argument to make given that whatever facts available at the time could also have been spun in favor of Gillett and HIcks, who at the time appeared united.
I'm not sure why you use Mourinho as an example of someone who managed their way to titles while his position was questioned- they have been unable to take back the league ever since his relationship with Roman soured, and now stretching to two seasons (so far). One smart thing that Abromovich did when Grant was under question was to affirm his position with the six year contract. people laughed, but look at the stability it gave them at least within the dressing room. At our lowest point of the season, there was open dissension in ours. As for Ferguson, their takeover never involved a questioning of his position. He has given the Glazers a rallying point against those who wanted to break away and form their FC United. Rafa has emerged to be a rallying point, but only after being bloodied himself and openly questioned by all parties involved.
Maybe now we can be blase about the off field chaos because it looks like there might be end game in sight at least for Gillett. Let's not forget how quickly sides and positions changed within the last five months, which seems like a life time ago.