Those senior civilian officials could be added to the command structure as needed when there are insufficient military officers to fill the available posts, or perhaps added anyway as an extra source of senior commanders. The civilian stats would be restricted to those applicable to planetary or sector government and they would follow a different "career path". Their terms would be much shorter, perhaps only a few years, before they moved on to other civilian roles outside the scope of the game. They would be placed in the commander window for convenience but would be flagged as civilian and would not affect the military command structure or the promotions of military officers. I would have to play around with the mechanics but how does that sound in principle?
Sounds like a way to work the observation into game mechanics, which is why you're the game designer and I'm not
So it sounds like the proposal is to count the number of high-rank governor slots available (e.g. R4 or R5 and higher), and "flesh out" the population with civilans up to e.g. 1.5x the number at each rank. I think I like it - it solves the "pyramid" problem.
Here's a more extreme thought - for governor slots for which civilian governors are being produced this way, require that any officer who's going to be the governor to retire out into civilian status (e.g. what happens in the Mote in God's Eye). This would emulate a "civilian control of the military" philosophy, and presumably wouldn't apply to worlds in the more oppressive political states (e.g. those that really would have a military governor). Also, you might want to couple it to government type (with switches to turn on or off for the "player race"?). If you went down this road, I wouldn't want my favorite senior military officer, whose career I'd followed for years, to suddenly disappear though due to quick civilian retirement.
Another thought - a pair of government skills for quelling unrest, one through oppression (e.g. internal police skill) and one through popularity (e.g. charisma). The oppression one could improve the productivity numbers at the expense of slower motion to the next political state (or even motion away), while the popularity one could move a population in the direction of rebelling against the empire (once you put internal political dynamics in place).
The "player race" switches comment above gave me an idea - why not change "player race" to a flag which adjusts the stats of the government type, rather than making it a government type of itself. That way, there could be differentiation within the game (not just within the role playing) between running a democracy vs. autocracy vs. communist state. This could be useful once you put political dynamics in place, or even if you want to assign advantages and disadvantages (beyond those during setup) to particular government types.
John