I don't think it will be the Thargoids, to obvious. Plus in the original elite it was hinted that it humans that started the war with the Thargoids.
I think what ever destroy the Guardians, is what lies beyond the Formidine Rift.
The AI was probably worried about its own survival, so it probably decided that the best way to survive was to commit massive genocide and wipe all of the guardians out (
"It's the only way to be sure.").
However, there was mention that the Guardians who ended up losing the first civil war were in fact exiled (so are likely to still be alive) - and these were the Guardians who favored closer relationships with their AIs.
The second civil war was basically the religious uprising across the entire Guardian bubble rather than the home world - this was basically to force all city-states across all colonies to submit to their religious doctrine. City-states being city-states, they would have had a hard time defending themselves against a unified planet with many city-states. They wanted to rid the AI from their culture, but they had also forsaken other technological integration and medical benefits (that likely made them more susceptible to diseases as the war carried on for over a hundred years).
I think it is very likely that at least one faction of the Guardians is still alive (the non-religious group), but they favor living in Witch-space (either because of fear of persecution, or because they know there is two factions of AI - the one they sided with and work with, and the other that decided to wipe all of them out).
There are probably two factions of AI - one that is good (perhaps caretakers of the Guardians) and one that is bad (perhaps the AI that wiped out the Guardians in normal space).
The ones that hyperdicted pilots are probably the good Guardians, since they left without killing anyone, and were probably confused by the radiation signatures of the Unknown Artefacts or Probes that mark human ships in some way.
The crash sites are, probably, clashes between the bad AI involving humans whom were potentially transporting the same artefacts or probes - but had bad luck of the draw in what AI hyperdicted them.
And if there are indeed two AI factions, with Guardians backing one of them, then both sides could both still be at war - though it is likely more of a cold war with scant skirmishes than an open war.