How do protection circuits deal with instantaneous voltage?
If the voltage applied is truly instantaneous

It can't be, so the premise of your question makes no sense and the question can't be answered.

Think about it.  A instantaneous step change in voltage would require infinite current to charge up whatever inevitable capacitance there is.  Just like there is always some parallel capacitance, there is always some series resistance and inductance.  Voltage simply can't change instantaneously.  Put another way, the derivative of voltage can't be infinite.