I've been wanting to chime in on this subject for a while now. In fact, waaay back from when you did your Fire Brigades mod.
I do all I can to avoid building ANY building with an upkeep percentage increase. This is because the perception of these increases doesn't seem too bad when you initially get the ability to build these buildings. But as stated, when corporations begin to spread they become ultra lethal overnight. Its not so bad since you can destroy the buildings once corporations come around but that's a very time consuming and potentially buggy process, so its better to just not build them, graveyards, public pools, fire halls, etc... all of it. I avoid it all and try to solve happiness and unhealth problems through other means. Because if I don't, the upkeep will destroy my economy down the road. I mean, if you build just a Fire Brigade in every city it will literally cost you thousands of gold per round when corporations are fully spread.
This means that while the concept you're working under appears balanced at first, thanks to getting some gold bonus buildings to balance things out, in the long run, it doesn't.
The idea of upkeep does include bureaucracy at work but it also includes crime rate and the effect of chaos (thus why courthouses reduce % upkeep). The only way to go back to rebalancing these buildings is either to give us enough buildings that reduce upkeep percentage or to give them a flat rate gold upkeep. The latter seems a good suggestion considering that this will make them a bit more appropriate for the earlier game too. That would make for an easier way to balance them overall as you can put into play a roughly equivalent subtraction of gold to the additions of gold you've included. In the early stages, the percentage upkeep actually does very little and is not costing enough.
At the moment, I'm at the tail end of the rennaissance and I'm pulling over 3k gold per turn on 100% research on Deity level play (increased to this level gradually). Since corporations aren't in play yet, I have very little upkeep and a lot of buildings bringing in gold. Once I get corporations out there, if I'm not careful with what I choose to build, I'll drop down to about 80% research to stay in the positive. In simple BtS play, corporations, if done correctly, will give me a net profit.
I love a lot of the new buildings but this issue really needs addressing and reconsidering! It should not be better to avoid building water departments and fire brigades than it is to build them. At the moment, it is better not to build them and allow unhealth if needbe.
It is assumed that zero will never happen but you seem to achieve it. 
but your the python whiz.
