So I think there is one conceptual flaw in the new system that we could consider. A big lever of the system is turn times, how many turns will a given mission take.
Ultimately though there are too many things that impacts, from the bonuses of certain buildings like the National Intelligence Agency, to CS quests, to the amount of tedium for the player. Now we could try to tweak and shift and prod and get the turn times just right...but I think that's barking up the wrong tree.
The CS rigs already has a unique mechanic. The rigs happen every X turn, and they all occur at the same time. Simple and consistent. Why not have spy actions do the same? Why not just add Spy events into that rig cycle?
So in this model, spy actions trigger when the CS elections occur. All spy missions have the same length, though the risk of spy death and detection do vary. The yields are made appropriate for this timeframe. The player deals with their spies all at the same time, and then doesn't worry about them again until the next cycle, providing a nice steady rhythm to the game.
Then security reduces the mission benefits, as well as increases the chance of spy death and detection. I can get a lot of gold out of a vulnerable Security 1 city, but Fort Knox is just going to be tricky. In general the player is incentivized to put spies in low security cities (which just thematically makes sense, you would always want to investigate the vulnerable places), but on occasion will want to brave those high security cities for a production disruption of a wonder, or a city defense disruption, that kind of thing.
This provides a solid baseline, we know how often players will get spy bonuses over 50 turns, and so we can adjust the yields very easily to create proper scaling. This further allows us to adjust the NIA and CS quests to easily accommodate the new model.
While highly variable turn times can look interesting in theory, in just one play through I am already seeing the problems. I think removing that as a lever, and focusing on other areas to adjust, will make for a superior system.