If you play the same stuff all the time it gets boring anyways. It's good to have something that makes it desireable to finish the game. In Aftermath you had the cultists taking over another land in case they get eradicated, leaving the player a thread at all times.
Also there was biomass covering large parts of the earth, which is kind of like our virus ideawise.
Well I think it's a good idea if there are ways to keep it under control if you don't mess up completely and let it go as high as 90% or whatever.
But imagine what happens if aliens take over a nuclear superpower state? Chine, Russia, USA = The End?
Well no but just consider that hostile nations are a massive thread and lead to a world war.
But in the end it's just a game mechanic so I'm not worried