Low current RPi GPIO inverter
I read your question twice but couldn't figure out how it's all supposed to work. A truth table is so much easier.

Anyway, it seems you want a logic high when the Pi is off and the ability for the Pi to switch the input low when it is powered.







simulate this circuit &ndash; Schematic created using CircuitLab

Figure 1. The interface.


R1 is a pull-up and holds IN high when Q1 is off. There is no current drain in this condition. 
When the Pi is powered the GPIO controls Q1. Set the Pi's GPIO high to pull IN low. (This may require inversion of your existing logic.)