This thread should help explain how the new system works:
https://groups.google.com/forum/?fromgroups#!category-topic/beagleboard/beaglebone-black/pf1MNKptqS0
In short, you can’t do that anymore. The pins are either set at boot time with an altered device tree binary or they are loaded after boot in a specific way using device tree fragments. You can’t just go alter the pin config registers yourself anymore in the 3.8 kernel.