Clearly you don't understand what the game actually tells us:
You'll notice a lack of "Ellie is immune" here, instead it's the cordyceps that's mutated.
The surgeon's recording:
-The fungus in Ellie’s brain hasn't spread to the limbic regions but is still present
-Antigenic titers are high
-In vitro fungal cultures from Ellie’s blood grow cordyceps
-No leukocytosis
-No pro-inflammatory cytokines
This points to the cordyceps in her brain having mutated to become an inert version rather than anything Ellie's body has done. She's showing no signs of her immune system attacking it, she's still infected but it's idle.
This means that the doctors need this new strain of cordyceps to clone the mutation, see if they can cause the mutation to happen in people infected with the classic strain and more importantly create a vaccine that would, essentially, infect people with this new strain so that the classic, dangerous one can't.
But for all of this, they have no need of Ellie, just the mutated cordyceps strain.