I have a similar issue in my current fort. After cleaning out the spoiler, one of the clowns had dangerous blood that's now been tracked outside and is covering my entire entrance area in addition to a great deal of my constructed roads. Luckily the blood is mild and only causes some blistering of bone that eventually goes away, but keeping the dwarves clean is a nightmare (dwarves spam clean self: area inaccessible when they try to use soap, and only clean themselves at the well after attempting to use the soap that's become forbidden), and the injuries by the blistering cause cancellation spam by haulers.
It is somewhat annoying that the issue could be worked around in two ways: either a method to direct cleaning, including cleaning things aboveground (especially constructions above ground), or dwarves equipping their clothing properly so they don't become infected by contaminants (nearly all my contaminations appear to be on their feet from walking through the killing zone). As it is my entire fort is naked, because their clothes have rotted away but they do not equip the new clothes they claim. I guess I could draft all the civilians and give them uniforms, perhaps then they would clothe themselves, but it is pretty excessive management for a fort of 120+ dwarves.
An interim but labor intensive solution is to build (or deconstruct) the tiles that are contaminated, though it means busy work hauling the trap components away and then rebuilding them, not to mention the road.
Guess I'll pick up DFHack to clean it for now.