Hi Rob,
You're perfectly on point that your circuit it will work just fine. The Netduio's digital pins are 5V tolerant even though they operate at 3.3V. That is to say, they output 3.3V signals, but will accept 5V or 3.3V signals as input. That said, it certainly wouldn't hurt to go with 3.3V, it will even save a miniscule amount of power (though really, not enough be worthwhile is all but the most power sensitive applications). As a word of caution: the Netduino's analog pins, when not operating as digital pins, are NOT 5V tolerant, and using a 5V signal could damage them. To be safe, I try to only use 3.3V signals with the analog pins.
As a point of nomenclature, a resister tied to ground is a pull-down (down to 0) and a resistor tied to VCC is a pull-up.
Good luck!