The biggest problem I have with the whole disease thing is that S31 allowed Bashir to know they did it. Bashir almost certainly would have been able to figure out a cure - maybe not in time to save Odo, or even the Founders in general - and he would definitely have suspected S31 (he did, after all), but they confirmed it. Bashir is the most TNG-ish of the DS9 cast (even more than O'Brian and Worf, somehow), and so of course he has to go on some big moral crusade - and the worst of it is, he told Odo.
Now the Founders know exactly how everything went down. Sure, the Federation gave them the cure, but they were also the cause of the disease. You know that a bunch of the new, exiting diseases Bashir goes on to cure after the show have to come from the Dominion, seeking revenge, no matter how much Odo is influencing them.