Certainly it seems like total eradication is the best option. The article just posits that one-off killings have a negative effect.
Knowing that the partial killing of a rat "family" potentially increases the diversity and potency of bacteria seems like very useful information in a world where we can't easily kill all rats.
Near the end of the article it mentions that existing rat populations act as a buffer against invasive species carrying new infections. This is pretty important for port cities, probably less so for inland areas.
I'm surprised they didn't mention it in the article, but Alberta (a province adjacent to British Columbia on the east side) is mostly rat-free (infestations per year at 0 or in the low single digits since 2000. It is entirely land-locked though. As far as I know there have been no adverse effects. They started aggressive rat control in the '50s.
Knowing that the partial killing of a rat "family" potentially increases the diversity and potency of bacteria seems like very useful information in a world where we can't easily kill all rats.