So far the method of pulling the staircase aside, sledge hammering the fence segments where the stairs should be, then moving the staircase back has been working for me.
My most frequent lazy way of dealing with this issue is just to shift+click teleport my sim past it (I think you may have to have testingcheats on for this). I've also just added a ladder sometimes, and this seems to properly create a break in the fence visually and physically. Granted it looks stupid but I was getting tired of seeing the female townies walk with knees squeezed together after a night of partying because they couldn't get to their restroom on the upper floor.