Slabs don't do what you think they do. A slab is just a memorial stone, that can be engraved with someone's name. It counts as burying them as far as preventing hauntings and negative thoughts in their friends, but you don't need to have access to the actual body. Slabs will not block water flow.
As far as cutting the aqueduct, screw pumps are probably best. Yes, they pump very fast, and should be able to beat the river, though you can just build a second one if the first isn't enough. Having them being dwarf operated is easiest, and works alright, but the pump operator will probably wander off to get a drink when your dwarves are repairing the plumbing, drowning them all. Putting a water wheel or two in the river and hooking it to the pump with axles and gears would be much more reliable, but is more of a pain. Using caveins to drop a plug would work, but is a pain. Pouring magma on it to seal it with obsidian would also work, but is even more of a pain.
For future reference, make your aqueduct go through a diagonal opening at the same level as the top of the cistern. This eliminates pressure, so your cistern will keep itself full, and can't possibly overflow. Also, use raising drawbridges instead of floodgates to block the aqueduct. Yeah, floodgates sound like the obvious choice, but raising drawbridges aren't destroyable when raised, and so are much more secure. Running the aqueduct through a fortification also is a good idea, but submerged fortifications are sometimes passable (I think only when there is active water flow. Creatures can be washed through by the flow). I got a herd of Elk Birds in my well room the other day from that issue.