Found a minor bug.
You changes .txt reads:
-Removed GP from divine right and returned its price to before (1200 instead of 1300).
But the cost for Divine Rigth is set to 1000 now, instead of 1200.
Thanks for that. Now fixed for next release.
Regarding the granary, I did originally hesitate to increase its cost. It doesn't look like it's supposed to be incredibly expensive and the change is not significant enough to have a major impact on strategy. As you said, a city with high food and low hammers is still going to build one very quickly for the more efficient whipping.
In general though, I want to tone down the strength of the whip. IMO high food cities have no drawbacks at the moment, when slavery is permitted. Slavery should be an effective way to convert food to hammers in cities but for it to be more effective than an actual hammer improved tile like a plains hill mine is a bit skewed IMO.
Previously I have tried fiddling with the granary's boost, reducing it to 30% of food stored or somewhere around there. Alternatively, I once tried increasing the whip anger duration by 50%, for 15 turns at normal speed.
What about if I decreased the granary's bonus to 25% of food stored, but gave another 25% to the supermarket?
Or maybe there are better ways to reduce the strength of whipping? For example, would it be a good idea to prevent whipping of any units, and only allow buildings to be whipped? At first I don't like this idea because it would be hard to get used to. Being able to whip an archer on short notice would no longer be possible, for example.
I could increase Slavery from medium to high upkeep, but I wonder if this is likely to have much impact? At the moment I'm feeling this is the best way to go, and reduce the granary's cost back to its original 60

.
There are of course many other ways to nerf Slavery by giving it more drawbacks, but generally I think most of the civics were designed to give positive effects rather than negative effects. I remember the first time I tried the Final Frontier mod and looked at the leader traits, that many of them have drawbacks as well as bonuses. The drawbacks were enough to make me dislike the trait even if it was still the best.
I am also reconsidering the +1

on farms for serfdom at the moment. It doesn't seem all that good when the -25% GPP is kicking in as well. By the way, I'm not even sure the -25% GPP actually applies if it starts from 0% anyway. In other words, if you have no great person modifiers you don't get the 25% reduction, but I can't confirm this yet.
EDIT... Just checked, the -25% does indeed apply all the time.
I'd probably increase slavery from med to high upkeep and at the same time give a different boost to serfdom than the current +1

on farms and GPP reduction. What about if I gave +2

to castles under serfdom? What about +1

for villages, hamlets and towns (but not cottages)?
+1

for farms? This one might warrant moving the upkeep from low to medium. My concern with this one is that it would make caste system look a lot worse. I don't use caste system much anyway, but I wonder if it would still get used? If not, I could at least decrease its upkeep to low.