What does this mean
The reasons for not doing the vaccine anymore were, essentially, "the vaccine is more dangerous than the sickness" and "the vaccine is not necessary to avoid the sickness".
Both of those statement are, factually, scientifically, not true. That's reality. Which is what parent meant, no matter the deep conviction and the political innuendo, ultimately reality is you either do the vaccine and are safe for no risk or you don't and you get infection waves.
It also makes a stupidly-obvious tactic viable for the enemy.
There is also the legend of sieging cities by catapulting diseased cows over the city walls. And if anyone knows the citation for that story, I'd love to see it.
Smallpox is a can of worms. But if you learn your enemy are idiots and don't have a flu vaccine, and you know your own forces do, I don't think you're going to get yourself sanctioned by your trade partners for exposing them to the flu. It will take out a statistically-measurable fraction of their troops, at a predictable interval, something you can plan to exploit with manoeuvre.
[1] https://en.wikipedia.org/wiki/History_of_biological_warfare#...
See: viruses and the efficacy of vaccines thereupon.