The healers in Aleroth did not assume the well was the source. Starting a new game Joram mentions that the healers lost contact with the source (the shrine still being accessible, though inactive), and Goemoe makes a clear distinction between the source and the healing shrine.
in divine divinity no, no they didnt, in divinity 2 however they 'do' assume that shrine is the 'source' over the long years between the 2 games they have forgotten how to connect to the 'true' source and instead depend on the faint trickle of its power that still slowly gathers in that ancient magic fountain. manifesting in healing 'orbs'
