So, you've all probably noticed that some poison effects spread due to the buggy liquid smear system (if not, there's a great description here
http://www.bay12games.com/forum/index.php?topic=54659.0). The player there actually used the burrow system to institute quarantine.
Personally, I think the idea of infectious diseases is too cool to fix; furthermore, you could make effects that take advantage of it. One rather difficult to program one could have a semi-serious effect, but also give the dwarf the same poisoned blood trait- so if that dwarf was ever injured, the disease could start to spread again.
Or, for what I think would be a really easy example, an effect that causes the dwarf to go berserk- the effect is already in game, seems like it would be easy to add it to a blood effect, and then you'd have the RAGE virus from 28 days later, down to waiting for the infected to starve to death. Imagine your champion coming back from fighting a forgotten beast, only to go crazy and start attacking your other dwarves, spreading more of the beast's blood around- eventually half your fortress is infected, and the remainder have walled themselves off wherever they can, maybe in significantly-sized burrows, maybe just one or two dwarves hiding in a workshop, trying to find some way to get food to them without exposing them to your crazy axe-wielding champion.
Might be a bit nasty for vanilla, but you could at least have some sort of "madness beast" whose breath weapon causes your military to briefly tantrum, attacking eachother instead of it... and then the modders could make the cool RAGE virus stuff.
Edited for clarity and removing ideas that weren't too related.