Most of the core deities are in Starfinder, so I think we can discard them. Maybe they get revived or Starfinder is an alternate timeline but I'm not going to assume that.

That leaves 9 deities: Erastil, Gorum, Gozreh, Irori, Nethys, Norgorber, Rovagug, Shelyn, Torag.

I think some of those have explanations of why they aren't in Starfinder. Torag I remember reading is guarding Golarion, wherever the planet is. Rovagug is either The Devourer or still inside Golarion. Gozreh is specifically a Golarion deity, so he/she is almost certainly still there. Erastil really doesn't fit Starfinder setting, so I think he is still around, but probably the people that worship him are not traveling in starships. Gorum and Nethys seem to be like weird choises to kill off, I don't think they are part of any current storyline and I can't really see the god of magic that knows everything dying, same with the god of war though he might enjoy that. Similarly with Irori and Norgorber, I don't think they dying would be dramatic enough.

So my bet is on Shelyn, it will probably involve Zon-Kuthon. And we already have the perfect replacement for the deity of art I think, Nocticula.