Definitely an interesting idea. Hypolimnetic aeration seems to be kind of a sketchy art, most of the discussions I can find on the internet center around using it in 100+ acre lakes and reservoirs, not <2 acre ponds.
You're right, it might be simplest and most reliable to pump water up, then gravity feed through a packed column and down through a pipe below the thermocline. Aeration could be done in a separate unit, either an attempted hypolimnetic aerator as detailed above or a simple bottom diffuser/thermostat setup.
Maybe the simplest set would be:
1. Well & pump -> packed column -> pipe below thermocline; with the well pump hooked to a thermostat set to activate when the bottom of the pond is above ~65F, and
2. Aerator & bottom diffuser; with the aerator hooked to a thermostat set to activate when the surface of the pond (perhaps 6" deep) is below ~64F.
Main concern would probably be, in the dogs days of summer, the bottom waters becoming O2 depleted but still cold. Perhaps the pump or aerator could just run every night for a bit, regardless of temperature.
This might be slightly more expensive in terms of electricity, but would be much simpler and have lower fixed costs than a hypolimnetic system. Pond position and construction would probably have a significant impact on how well this worked: a steep, deep pond on a north-facing slope with trees planted to the south should be ideal.
