Personally, I have a problem with the overzealous/dictatorial president taking power. I think it goes against the Utopian ideal of the Federation, and would be out of character for a career diplomat (which is what the President of the Federation Council is....the leader of a body of diplomats, not politicians).
Your campaign, your choices, but if you really want to do an analogy of what you think is going on with modern politics/mirror B5, you should adapt the idea to one of the foreign powers...maybe forgo the Romulan upheaval as portrayed in Nemesis, with the Endeavor's crew on an extended mission in Romulan space....with a new Praetor becoming unpopular because of his strong pro-Federation stance, causing a Civil War that the recovering Starfleet is drawn into.
Or, to get away from the major powers, have a successor to the Gorn Hegemony throne/leadership cause internal strife, with one faction calling upon Starfleet for assistance...drawing the Endeavor's crew into an extended mission.
The madman idea is interesting, but I'd like to hear it fleshed out...why is the madman after the CO; what is their history? Is the CO an NPC? If so, how does this affect the PCs?
Davy Jones
"Frightened? My dear, you are looking at a man who has laughed in the face of death, sneered at doom, and chuckled at catastrophe! I was petrified."
-- The Wizard of Oz