You can write it 4 bytes at a time by doing something like this:
nrfjprog --memwr 0x10001088 --val 10981692
Which is how I put a serial number in devices during development. Keep in mind that if you are using the newer bootloader in its default configuration it may be using the first two words of the customer portion of the UICR.
I should have mentioned that I know how to program 4 bytes at a time to UICR. I really want to know whether there is a way to program binary file of arbitrary length to UICR.
Not that I know of. I see two options that you might be able to use. Append the data to your hex file using the "mergehex" utility (you'll need it in hex format rather than binary). Or, write a script that does the needed nrfjprog commands for you.
