Messy midnight post incoming.
The more I think about how little compassion the narrative gives Jonah, the more baffled I find myself. Granted, it's what he would have wanted; I can't imagine being understood and pitied on a meta level would please him if he knew, but I have reasons to believe that was not intentional on Jonny's part. And that hypothesis momentarily discarded, we're left with the problem of why the narrative is so unsympathetic to Jonah specifically.
As an example, Jane Prentiss got compassion despite being a murderer because she was afraid and human, and that was an excellent narrative choice; the way Jon thinks back to her once he begins to understand what she was through is beautiful and doesn't lack subtlety. Why is that not the case for Jonah? I cannot see how he's any less sympathetic than Jane; she also attempted a ritual, after all, though she of course was unsuccessful.
Season five is when the narrative begins to split from the usual framing of avatars as complex and terrified; Annabelle being reduced to a mouthpiece for the Web when she had been hinted to be just as complicated a person as, say, Jon is a good example of this trend. Even Peter's reasoning was explained in the season four finale. And yet Jonah, the reason why the story even exists at all and arguably the most human of all the villains, disappeared for almost the entirety of the season only to be remorselessly killed in a five-minute scene. Yes, his last words left an impression, but even that was interpreted by some as being the original Elias shining through (I'm not objecting to this interpretation, mind you; I think it's interesting, but it does allow some listeners to further dismiss Jonah's character).
The lack of a humane framing of Jonah could be, as I said, interesting from a meta point of view given that in-universe he is a character who very much controls his own narrative, and it'd be fascinating for that control to extend to the audience's perception, but I'm reluctant to give Jonny credit for that. After all, if that had been his intention, he wouldn't have written Jonah dying begging for his life, now, would he?
It is dubious what they were trying to do with him: is he supposed to inspire compassion? No, Jon doesn't even hesitate, and the fans' reaction says quite a bit in itself. Is he supposed to be framed as purely inhuman? Surely not, as there are few things as sympathetic as a man terrified for his life. Is he perhaps a two-dimensional villain, and his death meant to be cause for celebration? But then, why is he the only cardboard cutout in a cast full of breathing, living morally complex individuals? And why is he hinted to have a much richer inner world throughout the podcast, then?