I suggest that after finding a cure for the virus, a injection-gun could be used for shooting the cure into infected humans.
About the injection-gun, it would be relative short reaching and require a good precission (lets say 30+). Also, knowing more and more about aliens, one should be able to load it with both alien-poisen-injections into it, which would either cause confusion or do serious damage to the alien (or maybe break down their natural armor, because it affects their skin). Last a heavy tranquilizer would paralyse the alien, and make it possible to capture it alive.
Special missions (just like UFO-crashes), would be available: When the government realise the virus is out of control, they call upon Phalanx to clean out a certain area. This would be god training for the soldiers. Civillian casualties will however make the union like you less.
(I cannot run 2.3 missions on my computer, so I don't know if these ideas are already there)
Sorry for the typos