Hi, instead of hacking SW, why not hack HW? Add one more extra NPN, so it will invert signal again?
Depends how brave you are, but there is also another (bit more dangerous) way - add serial resistance. Thing is that every GPIO suppose to have some protection diode (in generic - "every" IC - there are exceptions of course). They typically stand like ~1 mA without problems. I assume that your reset pin on Arduino have 22k pull-up -> use serial resistance ~1/10 of that -> 2k2 -> ~70uA leakage when GPIO on Rpi will be 3.3V. That should not burn Rpi's GPIO. When GPIO on Rpi will be in low, current will be ~200uA, but it will be leaking through switch transistor, which actually can deal with much higher currents.
But before you do any HW changes, make sure you made calculations (worst case) and all necessary measurements before trying on real HW. You have been warned.
When you think about attached schematic, it is just 2 resistors with 2 different power supplies -> quite easy math. If you're not sure, any free simulator can help you out.
Best regards
Martin S.