I agree with Alfettish.
Planning on replacing the rubber is a good move as you overhaul the rail, so cutting them would be fine. Actually removing the pieces attached to both the injectors and rail with those cups can be a chore.

A sharp and pointed hobby knife or surgical blade helps as there is little room to get to the length if hose hidden in the cups. In some cases I've used a dremel tool to gently grind through the hose ends to release them from the cups.
I've also opted to use quality fuel injection clamps on the rebuild just for ease in future removal. Good luck.