The hospital sort of works for now, it just wouldn't if you added new functionality. Dwarves really need to indicate it when they're seriously sick, the eye disease went unchecked for far too long. I don't think it's unreasonable to ask that the game be prepared to handle it if we add diseases that cause people's eyes to rot and make them shit their lungs out. That kind of warrants self-preservation at the very least on the level of the fleeing-from-animals stuff we have. It's primitive but imagine if we didn't have it.
So, now you're saying we need potential cures before we can have potential diseases- don't give us things we don't have the resources to fight?
If so, it's reasonable, and something I thought about a bit in my considerations of syndromes. The hospital system certainly could be adapted to work with this, though it might cause problems with Dwarven AI failing to recognize the differering severity of minor blisters and eye-popping diseases. There are certainly ways that could be fixed, as well- have a list of all the syndromes currently at large in your fortress, and let the player assign priorities, have priorities in the RAWS and don't let any randomly-generated ones be infectious, but that would, I admit, be more work for Toady. Eventually, I think, everyone would agree that we want both infectious diseases and a hospital that can handle them- but at the moment, I'd say the first is low-hanging fruit and the second is not. Maybe.
However, in the meantime, you could include only very weak- possibly limited-generation- diseases in the vanilla, if at all, and let the bolder modders handle the added difficulty of truly dangerous infectious diseases.
Example of something that could go in the vanilla, under my approach: an enemy has poisoned blood that infects a dwarf with condition A: Condition A causes the dwarf to have slow necrosis, and occasionally hack up bile (liquid B) - liquid B, however, only causes Condition B, which is just some minor boils and a non-infectious cough. While this would certainly add an interesting layer of difficulty to your fortress- finding and quarantining the dwarf with Condition A- it wouldn't have the capacity to be a true fortress-destroying contagion.
Or, if you do want real sicknesses, there are ways to make them more mild, and still fightable with current means- if you make the "bile" not spread like blood does at the moment, and keep the symptoms and chances of infection low, it could be handled by having more dwarves assigned to clean your fortress, so each pile of bile has less chance to infect new dwarves.
Last but not least, quarantine is still an effective option, assuming the disease has easily visible symptoms. Currently, most diseases will run their course- assigning sick dwarves to quarantine is very much an option, especially if Toady goes a little bit further and gives dwarves added resistance to diseases they've had in the past.
While all of that is going on, Modders could happily be adding in zombie-death viruses- I've heard a number of them express enthusiasm for such- and doing preliminary testing to see what the problems and opportunities with more complete contagions are.