You said that the diaphrams did not fix the problem. What is the valve make and model that you changed the diaphragms? How many diaphragms did you change? Is there a Master Valve you can tell this by the controller? What is the model of the Rotor Heads you are using and what is the nozzle in there? Rotor heads will use more water or Gallons per minute the higher the water pressure. If you have High water pressure and you nozzles would use 2 gallons per minute with 50 PSI they will use 6 gallons per minute at 80 PSI. This is just an example, but you get the idea. If you are exceeding the recommended flow through your pipe size you will get the water hammer. 1 inch pipe should only flow 15 or so gallons off of the top of my head. 3/4 pipe should flow up to 10 gallons per minute off the top of my head. 1/2 inch pioe should flow 5 gallons per minute off the top of my head. Also you don't want the water in the pipe to flow faster than 5 feet per second. This is why the pressure and nozzle selection is so important in how many gallons per minute is flowing through your pipes. The cheapest way to fix it is to buy new rotor heads and use the nozzle that has a chart that can tell you how many gallons per minute are flowing with your high pressure and stay with in you pipe size flow chart recommended flow as I have outlined above. The next is to use flow control valves. You probably need new heads anyway. Unless this all started when you changed the heads or paid somebody to change the heads that did not know what they were doing.
Good Luck