"rationale to this decision that I do not know or understand"
I imagine the rationale went like this:
We have intelligence that the soviets are developing weapons with deadly bacteria X with delivery mechanisms {Y, Z, ...}. We believe they can deliver an attack on this set of cities and we have this set of probabilities of stopping it. We've conducted experiments on animals and understand how X would affect an organism similar to a human. Now we need to figure out how it would spread through a city to prepare for the scenario where an actual attack took place. We need to test our metropolitan areas for spread by an airborne bacterium. Let's pick the most harmless bacteria we can find not native to an area and see how it spreads.
The framing in the article is incredibly biased. By no definition of the word is it accurate to call humans the subjects of the experiment.
If the risk of a bacterial attack was real, then it would be negligent not to prepare for such an attack, as it could mean the loss of tens of millions of lives across all metropolitan areas. The "subjects" of this test were not the humans, but the interaction of a bacteria and the structure of the city - to see how a similar but harmful organism would spread through a metropolitan area. These tests were not testing how these bacteria affect humans (it was known that they don't, and for the extraudinarily vast majority of cases, they didn't). As a matter of fact, the bacterial strains were chosen specifically because they have little or no immunity to antibiotics [1] and posed no known threats to humans.
1. http://www.nytimes.com/1981/04/15/us/judge-s-decision-expect...