Unless I'm missing something I think the Plague mechanic needs some TLC. I had a planet from another Civ flip to my control. Turned out that every citizen had the plague. Here are my issues with combatting the plague -
1) Only way I know to stop it's spread is to imprison plagued citizens and send everyone else to another planet.
2) The only mechanic to kill a citizen (that I know of) is to get the max planet pop below the current pop. However this only works if all citizens are plagued since you don't get to pick who dies. I have actually created a plague planet with minimal max pop and use transports to fill the planet with all my plagued citizens (up to 21 in current game). Eventually they'll die off.
3) The only other way I have figured out to get rid of plagued citizens is to load them on transports and use them for invasions.
4) The main issue I have is there is no notice mechanism for when a random citizen on another plant contracts the plague - that I have found. I have several planets which have had outbreaks since I got that first planet and if I wasn't checking it would have spread to their entire population. You have to manually scroll thru each citizen to see if they have the plague. This becomes a QOL issue and a real fun buster. A popup notice or even something on the planet summary screen would really help.
If I've missed something in the game it wouldn't be the first time so please let me know if I've been struggling with this for no good reason.