Cap off the well, just as a normal well has a bottom.

Put two permanent gust of wind traps on either side of the shaft beyond the illusory ceiling, opposite of each other and pointed up, diagonally, into the shaft. The crosswinds of both will rapidly accelerate the falling of the player. Seeing as how the victim is unlikely to be the first, there should be a pile of rotting and bloated corpses within the well. Fortitude Save to avoid being nauseated. The victim will first have to worry about drowning and then how to get out of the well with the gust of winds keeping him pinned in.

A clever PC really needs only to “lower” a rope into the well for him to grab onto and climb “up”.