The problem IMO is inherent in their approach - they wait to see how a character is received, bide their time and then if they're sufficiently popular or serviceable to an upcoming plot point, they bring them back. Unless they have a firm action plan in mind and commitment to definitively kill off a character, and don't leave it up to interpretation if they're "dead" or not, the temptation will remain there and will continue to do so unless they revise their approach. They probably don't really even see it as an issue.
With that said, I think they should cut their losses sooner rather than later, and irrespective of whether a character is brought back or not, if they are not working, find a way to exit them. Best done by introducing a new character in parallel who can take the mantle and then a decision can be made between the two. Sunk costs, and all that.
I'm basing it off Ishikawa's answer in the stuff from here.
Had his soul been destroyed before that point, she could've just said it, and yet she didn't. She just said he's in a similar situation to an Ascian trapped in an auracite and is implying that the auracite is less important than holding their soul still before striking it with the blast of aether. In conjunction with the fact that the white auracite method results in their "expulsion" to the Aetherial Sea (presumably to eventually be reborn), it follows that simply piercing the eye, which he was apparently within, is not going to suffice to destroy his soul, either, if a more comprehensive method cannot even do that. Just to clarify what I am addressing, it is not the consciousness - it is the notion that their souls are destroyed via the white auracite method. They're not, even if the EN version of What Little Gods Are Made Of gives the vague impression of it. Quite frankly we've no idea how his soul would be affected by what it's been through, so how his consciousness has been affected, whatever remains of it, is an unknown.
With that said, I don't disagree that that is an approach they could take with Pandaemonium. My theory on it is that it ultimately will provide a venue for the "what if" fight with Zodiark, since MSQ trials probably don't suffice to do a being of such power justice. I'm not particularly bothered by how they undertake further exploration of his character. However, his story did feel incomplete, especially with what we've learnt of him in Amaurot, so I'd like more of him, and possibly a proper boss fight, even if it's still a "what if" based on memory of him.