Why not capture some Vorta and Jem'Hadar, genetically remove the innate deference to the Founders, and even program them to kill Founders?
Considering the moral and ethical issues of 'programming' a sentient being to kill a specific group it would be something that the Federation shouldn't want any part of, Section 31 on the other hand... Removing the reverence would be another thing. Not sure how much it would matter to the Vorta given they have the power in the Dominion. As for the Jem'Hadar, their dependence of White would be something that would need to be dealt with at the same time. It doesn't matter if they don't see the Founders as gods if they are still dependent on the Dominion's supply of White.
The Federation could have attempted the strategy that was used on Stargate with the Jaffa. Give them the prospect of ultimate freedom and independence, with the understanding that the Jemhadar would have to fight their false gods in order to achieve this. The Federation should have been able to figure out the formula for the white. The JemHadar's violent aggresiveness would be a future problem, but really no more so than many other species.
I think their aggression is qualitatively different from that of other aggressive species such as say, the Klingons, and would have represented a huge problem. The one Jem´hadar who managed to live without the white and who seemed to have himself more under control, and have the ability to be more thoughtful and measured (raising the question as to what degree the white encourages their aggressiveness) was an anomaly, and despite his best efforts and their own stated desire was unable to change his subordinates. The Jem´hadar captured as an infant showed himself to be both unable and unwilling to change, and even Odo could not influence his behaviour. The problem with Jem´hadar aggression is that it doesn´t just represent one trait among many, it is all they are. They have been genetically engineered to functon purely as killing machines, and killing is all they want to do. They do not even feel the need to sleep or to eat. They have no interest in any pursuits other than fighting. There are no females so they cannot naturally reproduce. What kind of society could they ever build? Either you´d have to do some re-engineering on a massive scale, effectively re-writing their entire blueprint, or else they´d have to be eliminated. This would probably be the kindest thing to do. With the Dominion War over, they´re not really any use to themselves or anybody else.
I'm not certain the Federation has anything to offer the Vorta that they don't already have or want. They're already near the top of the Dominion power pyramid. They're genetically pre-disposed to view changelings as gods, and what more could a society want than to know that they are doing the will of the gods? "Freedom" and "independence" might not mean anything to the Vorta, and what more freedom and independence could the Federation offer than what they already possess under the Founders?