There is no danger (danger meaning potential damage) in powering off mid-calibration. Nor is there any danger in powering off mid-OS update (which I think is what you're referring to from the manual); you just might have to reload the OS in a special manner if this occurs. So, have no fear that power cycling will cause damage in any way, shape or form.
Regarding the oscillator calibration hanging, try disconnecting all MIDI/USB cables and footswitches/expression pedals that may be connected to the back of the synth. Then, clear the calibration data by holding both Transpose Up/Transpose Down and pressing Global. The first selection here is the option to Clear Calibration. Select this option. Then, navigate back to the normal global menu and try calibrating again. It may take several minutes to calibrate all 16 voices, but generally speaking it's pretty quick.
If it does not complete fully, contact our dedicated support channel and we'll get you sorted out.
One thing to note about the oscillator/filter calibration in the Prophet Rev2 is that it's a "set and forget" kind of operation, and for the vast majority of users, the calibration that's performed at the factory is the only one that's necessary for the life of the instrument.
I hope this helps! Do follow up and let everyone know whether or not this was successful for you, if you don't mind.