Yes, it's up to you to make sure that your system doesn't blow itself up when the MCU is in reset. However, are you sure that the pullups are active on reset? Usually the outputs are off entirely, in which case the the internal pulldown in the switches should keep them off. But resistors are cheap, and a footprint for a resistor you might or might not need is even cheaper, so I'd say put the footprint there in any case. If it turns out that you don't need the resistor, great, if you do, good thing you have a place for it!