Can regular Arduino pins be used during SPI?
I did not check the datasheet of the RF69, but it is customary for SPI devices to have a “slave select” input pin. When such a device is not selected, it will leave its MISO pin in high impedance and completely ignore whatever may happen on the MOSI and SCK pins. This effectively disconnects the device from the SPI bus. In this situation you show be able to play with the LED without disturbing the device.

Beware that the slave select pin is usually active low: write it to HIGH to deselect the device.