If I read this correctly, you are thinking about stratification in your pond. The idea is that becuase water has it's highest density at 4c, water in the lowest parts of a big body of water never becomes colder than 4c. This will be your lowest strata or layer of water, and on top of it can be colder or warmer strata.
Unfortunately, there are two problems. First, stratification will not occur if the depht is less than about 5m (which should about 15 to 16 feet). Second, even the movements your koi will be making are too much to keep the stratification in tact.
About using less flow, remember that less flow through your pipelines from the bd might cause debree to settle in the pipes, which might cause rotting, less o2 and even places for undesired bacteria to thrive. So IMHO, keep the flow.
Regenmeneer