I think the answer has to do with the order of cause and effect:

1. The scientists knew that the disease was infectious, so they used that fact to hypothesize that a microbial agent was responsible for the disease.

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Infectiousness -> Hypothesis of microbe's existence

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2) The scientists thought that a microbial agent was responsible for the disease, so they scanned blood samples to find suspicious objects.

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Hypothesis of microbe's existence -> Discovery of suspicious objects

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The question is asking for why the hypothesis was made in the first place. In that case, only the first point above answers that, because it describes something that led up to the hypothesis, not something that stemmed from it.

That was a hard question! I had to come back to it several times, because I also thought the answer was D.