First, that is total bull excrement about bypassing the heater. The more water you run though it the more heat you will extract although the temperature of the exit water will not be as high, the total heat absorption will be the same or higher - so don't worry about that.
If you are having water hammer what you could do is cut into the line and add a Tee in the horizontal position with the branch facing up. To that add about 12-18" of pipe and cap it. This will work to absorb the force and eliminate the hammer, this is done in piping systems all the time.
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