Well, I think what we need is a less vague spore system, then.
For instance, if a chamber is accessed on Z -5, then a tiny mineshaft unconnected from anything save the surface level on the far corner of the map should have no chance of the spores affecting that area.
In this way, one could contain the breach (after it is discovered that the Killer Spores were unleashed. Then it may be too late), and deal with any infected dwarves before it spreads. Likewise, uninfected dwarves could be placed in safe areas away from the breach, and a new fort could possibly begin.
As the system stands now, spores have infinite reach, infinite lifespan, and only need a flag (Spore=active) to spread. We would need actual logistics, even if they are simplified, to have this kind of feature.
Even better - the spores themselves could infect a dwarf's lungs, and upon death, the corpse could sprout the contagion's fungus to release new spores. While inside a dwarf, the spores don't spread?
And as for the plant monster idea, that's really beyond the scope of syndromes and so forth. Just the thought of having to seal away an entire established fort due to an infection (plant based) which stemmed from a forgotten cavern is awesome. Imagine a reclaim party/adventurer accessing the abandoned/sealed fort, only to find out that it would have been best left alone.
Anyways. I don't know. It just came to me while I was reading about cave fungus for grazing, and I'd figure I'd throw it on here to get other DF folks to think about it.