So this is just a shot in the dark, I'm somewhat new to the game, but why couldn't there just be a [FORCE_FLOW] tag to go along with the flow tag? It would designate any water with an artificial flow for its source. Currently I only know of the pumps. Any water wheel that was above water with that tag would not contribute any power to the system. (Conservation of energy wise it should actually be a huge drain, but whatever.)
So for instance, a 2 tunnels, one atop the other. Holes at both ends. A pump at one end, water fall on the other. Water wheel above the top tunnel. Assuming its connected to the pump, if you have a dwarf man the pump to kick start it, the second he lets go, the wheel (and flow) will stop, since the flow is flagged, and the wheel is contributing zero energy to the system.
Assuming you have your pump suck from an aquifer pit and dump into a river, we could have the regular flow tag supersede the force flow, somewhat like how salinity works, so the river would still work upstream and down to create energy.
I'm sure people are going to yell about the difficulty of getting power without perpetual energy, but it is an exploit, especially considering everything Toady is doing to simulate reality as close as possible. How about Geothermal? I think I saw a thread somewhere about that. Basically, you channel a pool of water one tile from a magma tube, and construct the plant in between the two? It would simulate the actual workings closely enough for DF, make perpetual energy a real feat depending on your map, heat engines are pretty simple so it wouldn't be an anachronism, (Unless you were to play a game running a couple billion years, but I'm sure someone's on that) and it's just more... Dwarfy. Humans build outside. Dwarfs delve, dammit!
Hell even just have a chimney from a magma surrounded room with water carry steam powering an underground windmill...