I think it's stated in the canon info thread (from the Kai Kennedy/Beowulf report) that Eliza was one of Great Mother Lamia's top generals, she betrayed Lamia, killed Aeon and Venus, and took over. Eliza's reign as the Crimson Scourge explains why people hate parasites (at the time, Sekhmet wasn't exactly secret). We don't know whether or not the Trinity was exactly nice to Mankind at the time; based on Double, probably not.
Speculation: There was a human/anti-Trinity revolution, which Samson/Delilah legitimately helped and Eliza used for a power grab. We know the Crimson Scourge fell
at some point, and Theons went into hiding and started being called Parasites. Reigning Theons were probably worshiped like gods while they lived (For darn good reason, given what Aeon, Venus, and even Eliza can do), so it would be easy for Lamia/now Double to co-opt the "old ways" into a new religion worshipping the same beings. Given how poor the current attitudes are towards Parasites, the Crimson Scourge was probably so bad that Aeon, Venus, and the Great Mother could be painted as martyrs who fell to Eliza's villainy.
Where the Skull Heart falls into all of this is kind of weird, given that Theons/Parasites somehow came from the Heart, but the Heart may have kick started the start of sentient life on the planet, so... I guess Mother Lamia was the first Being created after the Skull Heart fell to the planet, and it spawned Aeon, Venus, and lesser Theons, and eventually Ferals and Humans. This would explain why Double/Lamia/Mother are always connected to the Heart, moving it about and manipulating it, as well as why they'd want revenge upon all of humanity for their war against the reigning Trinity, Eliza, and eventually all Parasites.
Eliza wouldn't necessarily
disagree that the Trinity are gods.... She'd just argue that they're three mostly-dead members of a larger, once glorious pantheon, and for this she'd hate the current religion. Hell, depending on her tenure as Lamia's general, Eliza might even legitimately believe she deserves to rule Mother's empire, thinking she (Eliza) did all the hard work and got her hands dirty while Lamia sat high and mighty, all beloved and worshiped by a race of fools. Then humanity rejected Eliza's "leadership," and she decided it's too much trouble showing them their "rightful place." Better to retire to a smaller, safer spotlight, and have a nice drink.