Raspberry Pi 3 GPIO Input Offset Current Specs?
CMOS digital inputs are normally specified in terms of leakage current, rather than input impedance. I can't find anything specific to the pi, but normal values are around 1uA.

1uA*100kOhm = 0.1 volt, which is a small but potentially significant value. If possible, you'd want to measure the leakage current of the pi and choose a resistor accordingly. Your setup seems like a reasonable idea.

As a side note, the pi's inputs have an input pull up enabled by default on them (last time I was using one, anyways). Make sure you turn it off!