I guess I just would have liked a line in the script stating why there are no shuttlecrafts available in "Enemy Within" and then the episode would have played out the way it did with no shuttlecraft used.
Conditions on the surface would've made landing a shuttle dicey at best, plus the terrain provided no nearby landing sites, meaning that even if they could put the shuttlecraft down in one piece, a rescue party would have to move out from the shuttle in those horrific conditions to find the landing party and lead them back, maybe even carry them back, and then hope the shuttle can take back off without being slammed into a hill by the winds.
Now, while sending down a shuttlecraft before conditions got so wild may have been feasible, when you factor in all that time where they couldn't figure out what was wrong with the transporter in the first place, or how long it would take to fix it, and Kirk's overall indecisiveness, and by the time it was clear that the transporter wasn't going to be operational in time, sending down a shuttlecraft was no longer an option. And considering how fast the weather deteriorated, that window of opportunity was pretty narrow.