If you were comfortable modifying the NIOS firmware one really quick and nasty way to do it with really minimal modification and understanding of the command system is the following:
Assuming you don’t ever want to be able to set the VCTCXO DAC to 0 or 1, which is unlikely, you could add a if statement to the firmware in the place where the DAC is updated with the new value over SPI and in the case that it is 0 or 1, dont update the DAC and toggle the GPIO accordingly.
You could then flash this image to your fpga. On the PC call LMS_WriteVCTCXO(0) or LMS_WriteVCTCXO(1) to set the GPIO to 0 or 1 from your C++ code.
Its very horrible but if you need it fast it would work and only require the insertion of a single if statement into the NIOS fw.