Could it be considered possible for players to rebel against their High Council, and install others or themsevles, if they are not happy with the way that things have been run? Also what about inter-faction fighting, will that be something that is considered for the game?

Wouldn't really fit with the lore for the Imperium, Chaos and Orks this would be pretty nice though.

I suggested the same thing some time ago for Orks and Chaos. I'd like to see this system very much. An option to over-throw the leadership should be available only when the faction is in a weakened state, lost major parts of territory, etc. then the next highest ranking members of certain factions could organize small retinues and attempt to wipe out the war council, or challenge one of them to duel - winner takes all. War council would be able to create their retinues aswell, and if they got attacked by some over-throwers those players who are loyal to them would next time they died on the usual battlefield be spawned on the battle-barge to protect them. I imagine the war council would be stationed on Orbit on a battle-barge, so the fight and all would take place in the corridors of the ship.
I also think Orks should definitely have a player Warboss, next to their war council. Warboss would be able to both lead from the battlefield, and work as a part of the war council, but if he died he'd seriously demoralize the Orks in a certain area.