And now Adama forces the Cylon issue through marine imposition of Cylon crews over the objection of the President and the Quorum? Suddenly these "fleet security" issues emerge which can only be solved through immediate cooperation with the Cylons? They really can't figure out any sort of agreement over technology transfer other than permanent allliance? Besides, how can we forget that the only reason humanity still exists at all is that Adama kept potentially dangerous networking technology off the fleet, and Gaeta killed off remaining Cylon viruses. What sort of potentially destructive Trojan horses will this (completely not understood) Cylon technology bring?
To top it all off, this same military leadership failed to realize the existence of sleeper agents, and are bizarrely letting them remain in the fleet. In their reign of terror, pursuit of dictator power and love of secrecy, the Adama-Roslin regime has entirely discredited itself and needs to go. Without the false promise of Earth, and the end of open human-Cylon hostility after we jump away, it's time to move beyond military dictatorship--and Caprican overlordship--to a more permanent state of existence.
It's convenient from the point of view of the show's ideology to suggest that cooperation is the future. From any half-way reasonable International Relations view, this is nonsense. All the evidence suggests that the Cylons are simply a bloodthirsty race who can't seem to be at peace for more than a few days, either with the humans or even with each other.
You can argue about the necessity of a coup at that moment. Arguably, they could have waited until the superior jump drives were installed, or even until the Battlestar was fixed up. Then Gaeta could have launched his coup at leisure. Had they made a serious plan to grab the President, and shot the CO and XO on sight, it would have stood a far greater chance of success. Everything we know about military and civilian morale suggests overwhelming hatred of the Cylon. This is entirely expected; the humans are, after all, at war with them. Only the direct personal appeals of Adama/Roslin kept the anti-coup movement going; their deaths would have ended the struggle.
I'm ignoring, of course, the fact that the entire show should never have gone beyond the point where they discovered a virus which could destroy all the Cylons. If you find that; you use it and get out, and if someone stops you, you airlock them.