Personally, I think it would be much better if Bradeline's Well did not increase its plot counter until explored. I also can't think of any reason in the lore why a Well of Creation would be particularly evil unless and until someone messed with it. These Wells are passageways that the souls of the dead take to find their rest in the next life. True, the Well of Shadows was a rather creepy place before Auric destroyed the widdershins curse, but it wasn't particularly evil, that curse may not have been naturally occurring anyway (I suspect the involvement of a certain Once Elf Necromancer with allegiance to Laroth, but probably shouldn't be revealing this from the Ashes of Brigdarrow so I'll stop now), and that well lead straight to a part of the netherworld rules by Laroth. Nemora was probably the greatest paradise on Erebus until Tebryn closed off its well, thus forming the Dead Lands. It might even be appropriate to make closing off the well take more than just exploring it, as Tebryn found the runes and rituals needed to close of the Well at Nemora quite difficult.
Even though Bandeline was involved in demon summoning, his well clearly lead to the Netherworld and so it might also make more sense for it to be another course of Death mana. Normally it would represent the real death sphere and thus probably be opposed to undeath magic, but would be a powerful source of undead magic if closed.
It should be noted that permanently sealing a Well of Creation is a horrible idea, and certainly not something the Elohim would want. Sealing the wells seems to be a big part of Ceridwen's plan to destroy the world, hence her ordering Tebryn to close the Well of Nemora. It seems quite probable that souls that long for the next world would be led to Mulcarn's hell if the door to Arawn's dreamworld was locked to them, which is likely one of Ceridwen's main motives in wanting them closed and a reason why the evil gods have lately been able to collect far more souls than their due. The Elohim's sanctification of the well should surely involve opening it up again for the souls of the deceased to find their rest, rather than being eternally bound to walk Erebus after their time has past, turning them and the lands they walk into a nightmare.
It might also be interesting for undead units to disappear when they move into or near the well (unless it is explored/closed off), as the call of the netherworld to the dead is quite powerful when they are so close to it. It could also be interesting to somehow boost death spells cast here, at least once closed, as the spirits would still be drawn to the well but being unable to enter they could easily be captured and force to do a necromancer's bidding.
