I never use the native os, personally. The fact that it messes up the RTC was just the nail in the coffin - since switching to Dingux I just never needed to go back to native.
As for purging it from the nand, you can wipe the nand but you still need to run dingux off the SD card as there aren't any working drivers to get dingux to access nand at the moment.
At one point I went as far as writing my kernel into the nand (and making a custom SPL bootloader to load the kernel) so that there was no chance of going into native, and it also sped up the boot process by about a half second since I didn't need u-boot to load the sd card and read the kernel from it. But that was just goofing around.
Just use the linux-default version of the dualboot install and then you don't have to hit select any more.