although i think the major way you can get everyone to engage with disease plots more is by making disease protection gear more commonly available. otherwise, everyone just sits in their apartment until it blows over, which... is exactly what you're supposed to do, but it's pretty much just the death of roleplay.
Ex. Oh No! Someone let lose Disease X in NLM Tower! The WJF has cordoned off the tower for the next 24 hours while VS scrambles to make a treatment (or not, who knows if they made it in the first place). During that time, the people are all stuck in the location and plot ensues, be that just infighting or could be figuring out what happened, contacting people on the outside etc. Would be very interesting if a non-NLM member was locked in with them, all that.
I would always think that any City Wide plot should be opportunities for more people to RP. Any plot that requires you to stay indoors is... hard. It's mostly fine in that they don't happen often, but I like the creative ideas. Rage disease or Zombie disease would be really cool.
My idea would be something like Super Bedbugs or parasites that that spread disease from beds and couches. So instead of telling people to go home, they have to leave their apartments and cubes and deal with sleeping on the street or organize to stay somewhere safe, but certainly less safe than an apartment. Could be total Chaos, but possibly fun.
Anything that gives things for more people to do and be involved is great!