"The Search, Parts I & II," wherein we learned of the existence of Founder infants who don't know about the Dominion -- or about anything. You know, like infants tend not to.
The only reference to infant changelings in those episodes are to the one hundred that were sent off to "explore" the galaxy. There is no other reference to infant changelings.
And seeing as those specifically referenced in "The Search" were part of the special one hundred, we know they weren't
with the Founders at all
. So naturally
they weren't involved with the running of the Dominion. They were also naturally beyond the reach of the Section 31 morphogenic virus and beyond the reach of the war in general.
If I understand you correctly, it was wrong to attack the Founders because they had sent out one hundred infant changelings decades
ago? You're assuming that infant changelings exist in the Great Link on a regular basis, but I think that's a baseless assumption, because they're not humanoids, and don't necessarily have a distribution of "young" and "old", "leaders" and "followers". The idea that there would be "innocents" among the Founders is baseless, something you came up with out of thin air.
The Great Link is more like the Borg collective - there are lots of individuals, sure, but how do you separate them from the greater mass? Would the Federation be wrong to defend itself against the Borg because the drones are, individually, innocent of attacking them?
Should Section 31 have deployed the virus? No. Should the war have happened at all? No, clearly the whole thing was one act of aggression based on fear after another. However, since it was used, and since Section 31 did possess a cure, it did end up providing leverage for the Federation Alliance, and there's no evidence that any Founders died from it. Hard to be too broken up about the use of a weapon that ended a war when that "weapon" wasn't even as lethal as a photon torpedo.