I see a much simpler explanation... Section 31 engineered this disease such that Odo would be a "carrier" but not show symptoms... The disease would have been structured in such a way that Odo's morphogenic matrix was immune.
So he infects the great link, but since different changelings have different matrices (like DNA, let's say), they became infected.
But they made him human. No more morphogenic matrix, no more disease.
Then Odo encounters the baby changeling he purchased from Quark (and this must definitely be one of "The Hundred").
Baby regloopifies Odo, resulting in a ... *drumroll* new and different morphogenic matrix, still uninfected.
Then, Children of Time. No sickness (aside from love sickness, guffaw).
Then, Dominion Occupation arc... Odo gets the disease from Princess Evil, and is no longer immune because the disease is only engineered to provide immunity to Odo's *original* morphogenic matrix.
And they all lived happily ever after.
But why would they care if Odo gets infected or not?
And your idea of the different changelings having different morphogenic matrices is a nice idea, but in-universe it would contradict the female founder's claim that there is one Founder, and many, depending on how you look at it. If they had unique matrices, then there would be discreet individuals, and the drop would not be able to become the ocean.
So I think the evidence from the show indicates that as neat as your idea is, it's not correct.