The concept of bacteria causing disease had to go through the concept of Spontaneous Generation of Life. Just like today as we don't know what is life exactly in scientific terms. If we consider ourselves as living then viruses won't fit in the definition. How the life force get activated in the seed? Can we feel the heart beats in the seed ? The seed is alive or dead, how would you know that?

As we are learning through the science ( leaving the dream behind), we need to look at the evidences, and answer what we see is a fact or fallacy. To me, till we find and define the Thing Who Creates Life, let our believe and faith make a peace with the scientific observation. The same problem was there who suggested Germ Theory For the Diseases.

spontaneous generation:

This theory suggests the hypothetical generation of life from non-living matter.  Aristotle, a Greek Philosopher, observed that fleas are developed from putrid matter, that mice come from dirty hay, and so forth.

The Germ Theory:

The germ theory of disease states that many diseases are caused by microorganisms. These microorganisms first enter the body and grow by reproduction, rather than being spontaneously generated.

An Italian Scientist named Franscsco, in the year of 1968, opposed  the theory of Aristotelian abiogenesis ,and demonstrated that no maggots were bred in meat on which flies were prevented by wire screens from laying their eggs.

Louis Pasteur demonstrated that if the organic matters were first sterilized, and then prevented from contamination by microbes, the organic matter did not get spoiled, and the matter remained free from microbes.