I am a bit skeptical as to your solution. This is the negative production is the same method they use for a buildings maintenance, so thus I can not imagine that it is multiplied in the way you are thinking, as this would basically be counter to what they want from the multiplier in the first place.
End of kenata's quote
Edit: The negative production was not multiplied.
End of Heavenfall's quote
You are both absolutely right. It was a mistake in my implementation that made it look like it was working. Negative production is automatically separated from positive production in the city resource screen, and there's no way to fool it. (kind of makes you wonder they didn't anticipate the production of negative resources, like pollution, how about magical pollution that mutates your population into glowing mindless... ah well next time)
The good news is, I've actually found a way to build mutually exclusive buildings. No, this time for real! 
Basically set up a custom resource using Population as a template. In your city hub set a modifier for 1 resource per turn. Then set a resource storage again using Population as a template, set the storage value to at least 10x your accumulation per turn. See where this is going? Now on your buildings set a negative production per turn to about equal to your maximum storage (minus 1 needed for building it). The only real downside is that a player must wait at least 10 turns from founding their city before there's enough resources to build. Also there will be constant useless resource showing in your city screen. Each custom resource set up in this way can support an unlimited number of mutually exclusive buildings, however they will stay in your construction menu forever, even after the possibility to build them is gone.