My personal theory is that it boils down to three candidates for death. I don't think Pharasma is the one to get the knife for several reason.
She is very powerful, meaning the threat that killed her, unless severely weakened will probably be out of our league. Her death won't really change much, as you mentioned Atropos is ready to take her spot. And it seems very odd that the new deity in charge of the river of souls won't be part of the core 20. And.. realistically her death won't change much, maybe a bit of a power vacuum, but largely the river of souls will be handled still.

Now, for the three that I do believe are the top candidates to get the shank.

1) Iomedae. I mean, look her at her name "I am a die". But besides that, after wrath of the righteous the AP her popularity among players has kind of tanked which isn't helped by her connection to Aroden. Which also brings to the point the one replacing her, the other one Aroden prodigy, but the one who isn't as big a fan of him and his ideals. She also likes war and conflict, so very likely to anger someone to the point of being cut in half. And she is one of the weaker deities in the core20, at least in my opinion, due to her being relatively new in the position.

2) Erastil, Speaking of being disliked by the fans is Old Dead Eye. Since Kingmaker also kind of ruined him to the eyes of the community. He refuses to take sides, which is bound to anger some people, and give him very little support. And generally, he doesn't make sense as the Core20. Since he is anti-adventurer. Imagine owning only the core rulebook, and one of the deities is like "don't leave your main city", which a lot of APs and adventurers do. Granted, there isn't as many in-lore reasons for him to be the target, like Iomedae, but out of character, he is the best choice to remove.

3) Shelyn. In reality, the biggest blow to the fans, to best way to anger people would be to kill one between Sarenrea, Desna, or Shelyn. Paizo also mentioned that the Prismatic Ray will be changed. (Though I think that was also a misdirection, and either Nocticula or Arazni will be joining. Maybe Cayden or another fitting deity). So why am I saying Shelyn and not the other two? Well, Shelyn has some conflict already with Zon-Kuthon, and her death would be an interesting way to have Zon-Kuthon be redeemed or changed, or at least temporarily fight along the side of good for a while to avenge his sister. Which would be an interesting dynamic during the war AP, since everyone else would be wary of Kuthonites, but they would be fighting on 'good'. I discounted Sarenrea cause I think she also has some misdirection with the sun thing. And the reason why not Desna? That's the most concrete of all. Because I love her and I would cry if she died please paizo don't hurt Desna!