If high signal speed is not needed, you could just add a series resistor (with built-in pull-up disabled when MCU is running) to limit the current to low enough level where it no longer causes any problem. Current will flow through MCU input protection to VDD, and if VDD impedance is low enough, it won't significantly lift the voltage.
Clarification to this: if VDD impedance at 0Hz (so DC resistance) is low enough. Also known as: having enough load on the supply rail. And even more specifically, "dumb" load which consumes even below certain minimum voltage threshold.
Often these requirements are not satisfied, so even a tiny leakage current from IO pin through protection diodes slowly charges the capacitance on the supply rail, and after reaching some UVLO/BOD/whatever threshold, an IC (such as the microcontroller) decides to turn on; increasing power consumption and quickly consuming stored charge and dying again. The cycle repeats, making a slow oscillator.
This might not be a problem, but something worth understanding might happen. Simplest solution, if this happens, is to add "stupid" load such as parallel resistor between VDD and GND. It will then form a voltage divider with the series resistor on the input. If input series resistor is large (say 10k), then some added 1k on the VDD bus is probably not too much extra consumption - unless the thing is battery powered.
Or you can make sure the microcontroller does nothing dumb e.g. by adding a short delay in the boot where you do something power-consuming like turn a status LED on. It will brown-out and reset there instead of starting to do something.