Programing AVR 32u4 via ISP with other ISP device connected
Yes, that is possible and I've done the exact same thing with an ATmega328 which controls a DAC via SPI. If it wasn't possible ISP wouldn't be an option whenever SPI is already in use.
You should make sure that the NRF's CS pin is high while flashing the firmware, otherwise it might corrupt a checksum verification or memory readout.

Note the difference between ISP (in-system programming) and SPI (serial peripheral interface). Even though ISP uses SPI and they have similar abreviations they are not the same.