I don't know whether there's any way now to modify the effects of Exterminate, but I do know a way to solve your problem:

The extermination bringing in a lot of money is historical and not a problem. What IS a problem? Too quick of a resurgence in population. That's where you can really affect it -- for the cities that have too much pop growth, simply lower their farm values or make buildings have less of pop growth increase. That way you can exterminate a city, sure, and pocket a nice sum, but you'll leave the city useless.