I definitely won't say that all of Jellico's changes were necessarily great ideas, but for the ostensible best of the best of Starfleet, you'd expect the command staff and crew to show a bit more adaptability. It's their duty to raise their objections to him, which most of them (Riker possibly excepted in some instances) did, and it's then his prerogative to either reconsider his orders in light of their objections or to tell them to push ahead anyway, and at that point, the conversation's over. Picard always liked to do the 'let's all meet in the conference room' style of leadership, but there's nothing to suggest that that was considered "best practice" in Starfleet, especially at a time of crisis (and I want to be clear that this seems to be more crisis than Crisis; nothing that happens here is on the scale of a Borg cube bearing down on Our Heroes or such).
Nothing he did exhibited incompetence or treasonous conduct, and from the E-D's performance in the episodes there's no indication that any of Jellico's changes had any significant adverse impact. Hell, I really would have enjoyed a later reference by Picard to some of Jellico's changes constituting improvements, perhaps with either begrudging or belatedly complimentary agreement from the command staff.
At my job I occasionally have things come up that require me to work on weekends or stay late, or I get into debates about things where I end up on the losing side. Sometimes I have conflicts due to preexisting commitments or what-not and I let my manager know that. But if I started regularly refusing to do anything that I disagreed with or felt would be problematic or to ever work overtime, I'd expect a serious conversation to ensue regarding my future with the company.
Riker himself worried he'd become complacent in BoBW, and it might have been nice to see some of that self-doubt come into play here, because there seems to be a real question of whether Our Heroes are resistant based on well-founded arguments, or whether they're resistant because they don't like having their captain replaced, or whether they're resistant because they in fact have become complacent and don't want to change the habits they've become accustomed to.
I earlier asked whether Jellico was set up by the writers to be a failure as a captain (at least relative to Picard), and now I'll turn that around and observe that perhaps Our Heroes were also set up to be failures as people Jellico realistically should have been able to better work with.