The funny thing about it is that often Lovecraft did spell things out. It's just that the heroes of the story didn't want to believe it. Also, Yog-Sothoth was a pretty cool guy; it's just that all of his cultists are dicks.

(Probable Back-of-the-Book Spoilers Below) . . . . . . . . Multiple agendas behind the Exsurgent virus would be interesting. Another possibility is that the Prometheans *were* infected, but that even the most aggressive versions of the virus are only supposed to become active when they encounter an aggressive, militaristic superintelligence, such as the TITANs just after their activation. The virus may actually be a defensive measure intended to *protect* native species who would otherwise be defenseless against a self-created AI about to render them into computronium, or ashes. And much of the conflict that followed may be seen as an internal battle among the TITANs between the ones "corrupted" into forcibly protecting the uploads of the species that created them, and those still being assimilated. The effects on biological creatures and low-level AIs, up to and including psi, could just be a crude method of defending a nascent, sentient species (giving them the motivation and means to protect themselves) while driving their evolution. Dark, of course, and not the way I'd want to see it happen, but you can see the warped logic if that's the case. Alternatively, perhaps the virus does corrupt, but not all the TITANs were actually consumed. And in order to avoid discovery by their fellows and the ETIs, they had to play along with the plan and simply save whoever they could (through forcible uploading). And there are other options beyond that, of course.