Are you wanting to reverse the way the buttons function or wanting it to not start metering (and IS)?
If just wanting to swap AF-On and AE Lock (*) button functions...
Yes, you are missing something. Custom Function IV - 2: AF-On/AE Lock button switch. Set to Option 1: Enable. That swaps the function of the two buttons.
If wanting the back button to only do focus, then no...
When you have Back Button Focus set up on the 5DII, the back button you choose to use will also start metering (and IS on lenses that have it). A half-press of the shutter release button also starts metering (and IS). Only focus start/focus run is moved to the back button exclusively.
I really can't think of any situation where this would be a problem. Maybe if you told us what you want to do or what problem you are having, we might have a solution.