This is actually a different problem, in that /sys (sysfs) is a virtual filesystem and not actually something on the SD card. In that sense, there's nothing to save boot-to-boot.
It's also a deprecated interface, so you may just want to look into the newer interface.
If you do want to use the GPIO that way, you can do one of a few things:
Make a script that configures your GPIO on every boot (such as rc.local)
Write a udev rule that sets ownership of gpio files in sysfs
Just run your application with setuid root privileges
