So you're saying the soul cage was crafted in 1482 because that's when the dead three returned, but do we have anything in the game that corroborates that assumption.
As for the influence of dead gods...what is dead may never die, and with strange retcons...I'm pretty sure despite being dead (Bhaal was dead in the first two games) Bhaalists and the followers of other dead gods, have had influence and power throughout the timeline.
I don't think it's beyond the pale for Balthazar to have come in while Thorm was still Sharran, I don't think the followers of evil gods are barred from scheming with each other, and since we know that it was Thorm who captured Aylin, we know that she has been part of the Justiciar rite for what appears to be a long while