GPIO input protection
Running the DC sweep simulator made the voltage at Vout easily rise
  well above 5V.


The MMBZ zener diode is rated at 4.7 volts at 20 mA. At this current there is 19 ohms of resistance hence you can model the zener as a 4.32 volt device in series with 19 ohms and get a reasonable result. The 4.32 volts is as a result of reducing 4.7 volts by the volt drop across the 19 ohm resistor at 20 mA.

However, given that you cannot drive more than about 5 mA into the zener (24 volts/4.7 kohm) you will never exceed 4.7 volts.


  I feel like the simulator can't really function properly without a
  more detailed model and that the smaller 100mW package would probably
  be just fine? Would appreciate any thoughts on this.


Without a link to this device, darkness reigns over this question.