The CCU does indeed have protection for the aux water pump circuit, but excessive current draw from it can cause CCU failure. In fact when you buy a rebuilt CCU, they won't warranty it unless you check replace the aux pump.

To check the aux pump, simply rig up some jumper wires with a DC Ammeter in series. The pump should draw no more than 1.3 Amps. If you change antifreeze annually you will in all likelihood never lose an aux pump.

Good luck,