What we know about opposition to caste systems is this specific phrase by Sisko:
"You realize that caste-based discrimination goes against the Federation Charter. If Bajor returns to the D'jarra system, I have no doubt that its petition to join the Federation will be rejected."
Sure, Bajor's system or the discrimination practiced within it might be of a particularly damning type. But Sisko makes it appear more generic than that, that is, all discrimination that is based on caste is frowned upon in the UFP. Caste systems that don't
discriminate may be fine, though. How about a species of sentient termites joining? Making the workers do all the peacetime work and the soldiers do all the fighting would probably not count as discrimination if the very biology of the species makes such an arrangement the most comfortable one.
Certainly exotic biologies are acceptable for UFP members, even if the most exotic member species remain offscreen; but even purely cultural quirks are tolerated, and the UFP accepts that certain Vulcan males boss around their designated females and call it "tradition". Makes it highly doubtful that the Ferengi should be required to alter their sexist ways, either, in case they filed an application.
Then again, the phrasing doesn't yet establish that an applicant need be 100% compliant and compatible with the UFP Charter at the moment of filing the application. Perhaps there is room for adaptation later on - much as in "Rapture" where the absorption of the Militia into Starfleet is said to be an exercise for the time following approval of membership.