Clearly we can agree on there being a connection between the well and the temple itself, yes?
Seeing as I am currently re-playing through
OOT (Again) I will have my memory jogged in a not-too-distant-future, and will hopefully be able to make more sense of all of this, but I think I agree with the statement of the temple being a prison, and the well being a sort of back-up plan for those who either escaped, or just started to cause a rather large, bloody fuss in the village.
Am I remembering correctly in that there are numerous skeletons chained to walls in both places? NUMEROUS. SKELETONS. CHAINED. (to) WALL(s). Key words there. Sounds like a jail or torture-based setting to me. No one just falls down a well and somehow ends up in chains on a wall till death. They were put there, and KEPT there, for whatever reason(s). I am very hopeful that Skyward Sword will explain something about this, as well as many other questions I (and others) have, but that's a different discussion for a different thread at a different time.