One thing i have continually wondered is:
"Are contaminants effected by gravity?"
Currently i havn't tested this because i'm having too much fun in adventure mode to care about fortress mode at the moment, but if contaminants ARE effected by gravity, you can get them to fall through grates/bars and into an inaccessable area.
Take the water pool decontamination for instance; if you made the pool with the ramps replaced with stairs, and the stairs in the pool level up/down stairs with grates on them and another level below those grated up/down stairs, would the contaminants "fall" into the lower 7/7 pool beneath the grate?
TOP DOWN
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..>~>..
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#######
##X~X## 2-4 water level, grates on this floor
#######
#######
##<#<## 7/7 water level
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If for whatever reason the mess just floats on the surface of the water, could draining the water from the lower pool force the contaminants to move with the water, and fall down? If this is the case, you could 'flush' your decon pool after every use or get a repeater to do it automatically.
If contaminants are effected by gravity when washed at a well, the solution to piles of contaminated garbage on the floor is even simpler; remove the floor. You'd just channel all but 1 orthogonal position (so the well doesn't collapse) and replace those tiles with grates, filling the remaining position with a constructed wall (or natural wall, if you planned ahead) and so, all the contamination would just fall onto the ground below and become totally untouchable by dwarves. Of course, if water ever flowed over those piled contaminants, it'd literally poison the well forever.