I took a tally: 95 skeletons AFTER you've killed all the Baa-stards. And don't forget, you're generally lower than level 5 at this point. What I did was to run upstairs as quickly as possible. Only 3 or 4 skeletons will follow you into the hall. Upstairs, run to one side of the room, as close to the balcony edge as possible. Shoot as many as you can reach. Eventually, they'll crowd the underneath side of your balcony, where you can't get at them. Then you run over to the other side and repeat. When there are fewer than 20 left, just come downstairs and finish them off.
Dragoons' Cavern is a little easier: you can finish the quest without finishing the dungeon. (Just ignore all but the first batch of Oozes. I did come back later to polish them off, though. By that time, the rewards were pretty lame--but I could have used them the first time around.)