How to detect SD Card Insertion Without Leakage Current
I'm pretty sure the datasheet warning is there to cover the case where a pin is tied directly to Vcc or Gnd, but then the firmware configures that pin as an output and tries to drive it to the opposite state (either because of a bug or a subsequent firmware change).

If you really want to play it safe, put a relatively low-value (say, 1K) resistor between the card socket contact and the GPIO pin. When the GPIO pin is used as an input, this resistor forms a voltage divider in conjunction with the internal pullup that still allows the pin to be read as "0". However, if the GPIO pin should inadvertently be configured as an output and driven high, it serves to limit the current flow to a few mA.