I personally believe a good quality pump (Danner or Eheim) should last as long or longer than a heat sink fan. Usually with magnetic dirve pumps you will hear the shaft bearings becoming weak long before they fail (and the pump usually continues anyways).
I use MotherBoard Manager 5 (MBM5). You can add on a shutdown program and it appears to be reliable (I unplugges the pump and saw!), but still, I trust my H20 as much as I trust a HSF, it's a risk you gotta take!