You're correct. We know they fled Glyth, but we don't know if they ruled it prior to that. That they ruled it was an assumption that the text doesn't confirm. They could have been a marginalized minority population.
Drizzt Do'Urden's Guide to the Underdark, page 75. "Oryndoll is one of the oldest illithid communities. Founded over twelve millennia ago, the city began as an illithid enclave settled by refugees from Glyth, a Realmspace planet. After landing on Abeir-Toril, the mind flayers fled the sun for the cool Underdark. For nearly a thousand years the city, named for the leader of the emigrants from Glyth, slowly increased in size and influence."
Grand History of the Realms, page 14. "c. –11000 DR The illithid (mind flayer) enclave Oryndoll is settled by refugees from Glyth, one of the wandering stars that circle the same sun as Toril."
I think that's all we know, canonically. Given the time period, the idea that they were refugees from Gith's rebellion sounds like a plausible theory, but they could have been refugees from, say, a beholder invasion or something for all we know for sure.