It's a stretch to have his resignation seem like a bad thing, given that he was staking his career on a stand for what most people watching would think was the morally right thing to do. Resignation by ministers or military brass in the face of policy decisions and orders that they cannot accept is not an unusual thing and not an example of hubris.
If he stays on in Starfleet, the Romulans will still not be saved, and the synth ban would still be in effect. 14 years later Clancy still thinks it was the right thing to do. She may not like what he said in the interview, but how was what he said wrong? Retired Admirals and Generals in our world routinely take jobs as TV and media pundits giving their views on National Security matters, and this does include criticism of the policies of the current government.
Granted they never mention names of Federation Presidents and Federation Council members. There is just things like "Starfleet" referred to. A Trump like President would have helped. The Federation is not a military dictatorship. These policy changes would have been made by the Federation govt, not a room full of Admirals.