On the one hand, containing a plague in a post-FTL universe should be relatively easy: very few viruses can travel through space, so as long as Naboo was quickly and effectively quarantined, the danger level drops from "galaxy-wide disaster" to "planet-wide disaster." You can even theoretically bring supplies in with automated ships and droid workers, traveling in ships with the life support turned off.

On the other hand, seeing Naboo blockaded again, this time by the Republic, would probably exacerbate social unrest on the planet itself, given that the population is still recovering from Phantom Menace. I could imagine that the fragile peace between Gungans and humans would be put to the test, not to mention the potential for disaffected citizens/Separatist agitators making the obvious connection: the Separatists must have a cure for their own disease, so if we throw ourselves on their mercy, maybe we'll be spared?