Comment 3 for bug 699270

The add to DJ's workaround, you can actually get a "square" pad for the through-hole pin by using overlapping SMD pads. Simply make your pin as usual, and overlay an "almost-square" surface mount pad with it. Make this SMD pad slightly non-square to overcome the ridiculous restriction that prevents rotating squares (e.g., make it 70.00 mil wide and 70.01 mil long).

Make sure you use two SMD pads, with one having the "onsolder" flag set, if you want pads on both top and bottom of the board.