The script was originally structured so that the scene in which K-9 departs with the Doctor and Leela could simply be dropped if the character was not to be retained, leaving the implication that he had simply been returned to Professor Marius off-screen. See more
The virus has a perfect right to exist as a virus, not as a giant storm threatening the entire solar system. Everything has its place, otherwise the delicate balance of the whole cosmos is destroyed.
I still say we should blow it up.