Beyond level 10 resource buildings seem to reach a point where they'll take MONTHS to pay for themselves. They turn into such a resource dump they're probably better avoiding rather than investing in.
Take for example an L11 gold smelter upgrading to L12:
W=14284 S=8571 I=5714 G=9032 TOTAL =37601
Increase in production =39 (included the % increase from research)
assuming each resource has a 1:1 ratio (at the same level, they produce the same amount, except for gold which is a little less) that takes about 950 hours to match cost. Assuming perfect 24 hour collection, that's ~40 days.
This, combined with the negligible relative output of buildings compared to fighting, results in these buildings being better generally avoided.
As for a solution, Increasing their output (rather than decreasing their cost) would be a superior fix. (as well as avoid 'screwing' people that already paid a high price to upgrade them to a respectable level!) You could actually DOUBLE production and not screw over balance.
--Just remember, however much you increase production you should also increase their storage by an equal amount!