As you said, gold doesn't really make sense to me since the main way you will get them to be friends is to pay them large piles of cash.
Science would be duplicative of one of the Patronage SPs, IIRC. This may not be a bad thing, but it could lead to a run-away tech game if you doubled it up.
I'm pretty sure this would require access to the C++ code to do.
My $0.02 worth. One way around the cash problem is to simply down-play the importance of cash in maintaining relations with City-States, & instead play up the importance of *quests*. Another solution to both the cash & tech problem is to have the bonuses only apply to existing buildings &/or specialists, rather than a flat bonus (so, instead of getting a flat bonus per city, you might only get the bonus to an existing science building or science specialist). If we take this option, then I think it should apply for all City-State bonuses.
On another topic, this is how I would actually classify various City-States & the benefits they give:
Militaristic: Bonus XP to units built in your cities-grant you units on occasion.
Cultural: Bonus Culture to cities with a theater. Culture from trade routes.
Mercantile: Bonus gold to cities with marketplaces. Extra Cash from trade routes.
Maritime: Bonus XP to naval units built in coastal cities. grant you naval units on occasion.
Agricultural: Bonus food to cities with a granary. Food from trade routes.
Scientific: Bonus science from libraries. Science from trade routes.
Industrious:....well, you get the picture.
The only odd one out are Holy City States, which I think should work somewhat differently to the ones I've listed above.
Anyway, just some thoughts.
Aussie.