So, the floor is on level 85, and the cistern extends 15 levels up from there? Then the topmost level of the cistern is utterly empty.
Seeing as the cistern itself is huge, being past 10x10 in floor size terms, you could build a purely constructed structure hanging from the ceiling there and pump water into it. I think. The access point for water would be on level 101, though... If it's above ground, then you would have to make a walled-off area, if it isn't, then it's fine, right?
Say...
Level 100:
######D#########
000000F000000000
000000F######000
00000FF#7777#000
000000%X7777#000
00000FF#7777#000
000000F#7777#000
000000F######000
0000000000000000
0000000000000000
#s are walls, Fs are floors, % is passable pump tile, X is impassable pump tile, 0 is open space with water on the level below. The first string of #s is one of your cistern's walls. D is the access door to it.
Side view:
###########IIII####
00000000F%######000
77777777777777777777
I is your new water source zone.
I think that if the small room's underside gets wet with splashes from the Z-level below, nothing bad will happen.
Or just deconstruct everything.
My experience:
Left panel: Top level of a 9x7x2 microcline cistern. It is contaminated. It used to be not contaminated, but I accidentally caved something in on the pump before and it deconstructed, letting water on onto the natural black sand.
Middle panel: Kimberlite pump pumped water into a secondary microcline 2xsomex1 cistern. It is not contaminated.
Right panel: The 3x1 hole above water has a 5x3 zone centered on it, and it has 12 water source tiles. The hole leads to above the secondary, 2xsomex1 cistern.