Even if the operation you're running only uses one core, for many of us, the more cores still result in a speed increase. Looking at my dock, I currently count nine different programs running, add to that the OS and background services, and when I go to Activity Monitor, I count 58 processes right now. So even if a task isn't built to take advantage of multi-core CPUs, distributing all those processes between cores may often increase overall speed. Also, the number of programs that don't take advantage of multiple cores is getting fewer and fewer.
I'm guessing they are offering you the model closest to the price you originally paid. If clock speed is more important than core count for the software you use, you might try asking them to give you the single cpu, six core, 3.33ghz Westmere which is not that different in price at base configuration than the 2.4 eight core model.