Use devmem2 to change the value of the pinmux register
Make a special program that effectively does what devmem2 is doing in a more controlled way (i.e., memory map the address and do the modification within the program). This program could get the setuid permission to allow it to run as root and do the limited secure action of changing the pinmux setting.
Make a simple kernel driver (or modify an existing one) that makes a sysfs property that you can echo to that will cause the pinmux value to be updated correctly to the HSIO mode for UART support. I can’t remember which driver the kernel uses for the Tegra UARTs, but you could even hack in the necessary code in the driver to do the proper pinmux for the UART during the device driver probe operation.