I have a 12 MHz voltage controlled oscillator driving the nRF9E5 at pin xc1 and xc2 is open will this pose a problem for running the nRF9E5? The clock has a +-50ppm stability so perhaps the 915MHz radio transceiver would not function? But could it program and toggle a pin?
Your assumptions are correct. The CPU can run based on the VCO, and you can run code, but the radio will not work since the phase noise from the VCO is too high.
If you want to use the radio you would need a proper crystal.