How can I protect an input signal to unpowered CMOS?
The easiest way to deal with a digital signal like that is to feed it to a BJT or MOSFET with a pullup from the processor voltage. For example: 







simulate this circuit &ndash; Schematic created using CircuitLab

The diode allows the input to go negative as well without damage to the processor or transistor. Brief spikes of +/-100V won't hurt anything, regardless of the processor power state. Cost is pennies, at most.