I really like that Marc Miller's vision is an Imperium that will burn the surface of your planet to cinders if they feel it's in the long-term interest of their survival - shades of Foundation and Dune.
The thing about "Imperial entanglements" in Traveller is that they take time - weeks to months to years to decades to generations - due to communications lag. Waiting for the subsector duke to act could allow contagion to spread with every jump to and from the ducal seat. The first line of defense against plague ships is the SPA Health Officer and staff, but it's a thin line at best, since some proportion of traffic between and within star systems will not originate or terminate at an Imperial starport.
As a consequence, I think system governments take a pretty active role and response to the threat of contagion, and not just for people but for plants and animals as well, because if they don't, Imperial ortillery may ultimately do it for them. Local cooperation, at the level of one or two jumps at most, could be critical to containment.
This makes the threat and actual spread of disease a gold mine of opportunities for adventurers: delivering doctors and medical supplies for SPA or NGOs amidst a growing planet-wide panic, rescuing uninfected - hopefully - sophonts from an isolated community before contagion reaches them, transporting samples - samples others want for less sanguinary purposes - to important research labs for analysis.