Agreed.
The Emperor is not an absolute dictator.
For one thing, the Tyranny Of Distance (and thus, Lag) between Core and outlying sectors makes such an aspiration almost entirely unworkable in practice.
Not for nothing, but the "Tyranny Of Distance" affects the bad guys too.
Also, as I mentioned, no one knows if the Captain of the Guard who nearly gave his life and might have given a limb is only that loyal because the baddie has stuck to the Emperor's limits. Every would be Tin Pot Emperor has to worry about those assigned to serve in his court as a safe guard against any separation between the desires of the Throne and the target.
Added to that, distance shrinks if you have a covert layer of J-6 ships for the use of the government only.
This has already been hinted at, as a method of communicating alarms both locally and to Capital.
So, a casual check just before I wrote this showed a J-6 courier could make the trip between Capital and Rhylanor(Spinward Marches) in 26 weeks.
No, that is not insubstantial.
But, if the alarm is raised, it is only a handful of weeks before all major commands in the Marches AND all major commands in the Deneb sector are notified.
So, even as the message is on its way to the Throne, it is notifying all loyalist commands.
So, if a world has gone rogue.....the subsector commands will be warned quickly, a levy raised and action taken even as the Sector leadership are being told (or about to be so)
If a Subsector decides to go rogue, they have to first subdue any loyal formations in the subsector. So, there will be fighting already happening as the rest of the Sector fleets are raised.
If an entire Sector decides to go rogue.....there is much more in-fighting between loyalists and rebels
Even in the First Imperial civil war, most of the civilian Imperium just did their best to go about day to day business and hoped not to get sucked in....except the Spinward Marches, of course. (Sarcastic alert) They were dealing with fighting those peskey Zhodani (/Sarcastic alert)
And, in the MegaTraveller Civ-war (which I did not accept IMTU), the issue forced every command and every system to choose "who they'd support. So, fighting even started between military formations and the assets of the system they nomrally called home.
So,
1) There is a huge amount of consideration beyond simple distance and communications lag
2) You should check out my earlier post on this subject the other elements the Throne may have in place to stop just a thing
3) If you do keep your life vs Throne-emplaced assassins....and, you do gather a number of allies....you will soon enough face a massive wave of Imperial forces coming to bring your systems back in line after burning you and your last standnig loyalists down.
While there may be odds the above scenario won't work out, the odds are greater they will.....especially scaling up the smaller personal rebellion is.
The smaller your allied force is, the smaller a wall of warships and Marines will ha ve to be in order to burn you down.