There is no such thing as legitimate genocide. Ever. Species have a right to exist, full stop.
And what if a race consists of a single (remaining) person who is a mass murderer and attempting to kill others? Which capture is not an option? By killing him, you have committed genocide. *
Which is the essential problem. The Founders as a political organization are evil, repressive, cruel, and genocidal. Odo is not a Founder but he's a Changeling. The Changelings not involved in the Founders are blameless and infecting Odo to infect the Founders is an act of murder on Odo.
I liken it to the Doctor's destruction of the Gallifreyans who, during the last period of their life, decided as a group to destroy everyone else in the universe with only 2 objections. Every Gallifreyan is a criminal with intent to commit genocide on a massive scale. It's just so they're the last of their race.
Star Trek, of course, dodges this issue entirely and the Founders presumably learn from Odo how to be happy and peace-loving beings--which is probably a more realistic ending to the war and reflects what might happen in real life. In RL, you have to forgive and sometimes let bad people off the hook if it means more people are saved in the long run. That's how peace gets made and cycles of revenge are ended.
However, saying Section 31 is absolutely evil for their actions also ignores that the only reason the Cardassians are alive is the THREAT of the plague. The Founders didn't learn reason or compassion, they learned surrender.
Except that we know both from the canon, which established the existence of Founder infants, and from novels like The Dominion: Olympus Descending (which established the existence of Founders with minds not fully-developed and unaware of the outside universe) that the Founders are not all involved in the Dominion decision-making process, and are not all guilty of war crimes. There are in fact, what can only be described as Founder civilians, just like any other society. And we don't know that there aren't Founder dissidents who opposed policies but didn't carry the day.
I'm merely going from the DS9 series and my observations of it. Odo's position as a being divorced from the Great Link means he has a different perspective from the other Founders. That, other than themselves, they are unified in their opinions and ideals. I took them to be a Gestalt intelligence by the Female Changeling's description they are an ocean and only become drops by conscious will. In short, they're a hive mind like the Borg. Odo's individuality is a unique concept (or semi-unique) because he and the other Changelings "cast into the wind" are different from the other Founders.
The lack of dissent being based on the fact no changeling has killed another (or seemingly disagreed) until Odo.
Point taken, however, on the novels. I don't LIKE the message that Section 31 is justified in creating a WMD bio-weapon but I thought it was ambiguous since the only way to save billions of lives was through it's use. The mercy shown at the end of the series seemed "tainted" in a way that's never really acknowledged. For me, it seemed, "We can destroy you at any time. Stop attacking us."
* I'd like to also clarify in RL, there's no such thing as "tainted blood" and genocide is the vilest crime in the world. Any human being, no matter his parents or their actions, can learn to be a good person and "sins of the father" is nonsense. Thus questioning whether it's right or wrong to kill "purely evil" races like Daleks or destroying the Borg is a fantasy ethical question, of no real relevance in RL.
However, the issue of WMDs and the threat of their usage as well as letting war criminals go seems to have been papered over in the episode and intrigues me.