Use digital pin,both as input and outpout,without always reconfiging the pinMode

Form your initial posting.

settra:
the thing is, that the two relays must NEVER be closed at the same time.. arduino can do this easy via software , but if the user presses the switch (roll down) at the same time as the arduino is rolling up the window, then there will be short-circuit between the two relays..

This is simply wrong. That is my point. Understanding that removes your concerns about interaction between the switches.