This is an old theory which as you say has been debated endlessly. Viruses are not bacteria though, they invade healthy cells with the purpose of replicating themselves, thats it. They do not break down dead tissue. They destroy healthy living cells so that they can replicate and then spread out to more healthy cells. This is what causes the severe respiratory failure in some patients that are infected with such things as the swine flu virus. A virus is not even considered a living organism, it is a core of RNA or DNA surrounded by a protein coat, and it needs a host cell to replicate itself.
It is far from the process of bio-degeneration that occurs in the compost pile. So IMHO the germ theory does not apply in the case of swine flu.