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.
No conflict required - let's say the matrix is redefined every time two or more changelings "link" together. Pretty snazzily fits with the "ocean becomes the drop" concept.
It would also mean that Odo would be succeptible to the disease at any point after linking, but Sec 31 wouldn't care about that, as if he'd already visited the Great Link and delivered the virus, Section 31 would no longer have any interest in maintaining Odo's health to cover up his carrying of the virus.
But as a side note, I think you may be taking the Female Changeling's statement about the ocean and the drop a little too literally... While Changelings can intermingle unlike solids, I don't think they ever lose their sense of identity (as, for example, the Borg do) and they're clearly not a hive mind. Also, my sense is that if some number of changelings, say, 26, were to enter into a link orgy, the same 26 would come out again after. You wouldn't get 25, or 27. I also believe the population of the Great Link is comprised of a fixed number of individuals at any given time, even if they are all in liquid form together on the same planet, they could still be constituted out into the same individuals afterward.