I'm actually going to take this seriously and analyze what might happen. I do have to make certain presumptions, one of which is the unlikely notion that the Biblical text would be unchanged in an Omegaverse.
Acknowledging that plenty of scriptural texts get ignored, let's nonetheless start with some quotes from Paul. I Corinthians 7 goes into some detail about sexual desire and marriage.
8 Now to the unmarried and the widows I say: It is good for them to stay unmarried, as I do. 9 But if they cannot control themselves, they should marry, for it is better to marry than to burn with passion.
By this logic, both alphas and omegas have a mandate from God that they should marry. There is a high likelihood that they will in fact be married off as teenagers. (While it seems likely that for practical reasons the age of consent would be lower in an omegaverse, even by local standards they are likely to be married off too early.) I suspect both alphas and omegas are likely to be recognized as real biological variants. ("With passion" is a valid implication of the word used for "burn", but is not a separate phrase in the Greek text. Many people have instead assumed Paul means "better to marry than to burn in hell", and that is probably still in full effect.)
Many Protestants don't agree with the anti-sex interpretation of v 1: 7 (Now for the matters you wrote about: “It is good for a man not to have sexual relations with a woman.”) In v 26, Paul refers to a "present crisis" which they interpret as an outbreak of Roman persecution; in this environment, they think Paul is suggesting couples will get the Winston-and-Julia treatment from the authorities. I bring that up to point out that most low-church Protestants don't associate celibacy with holiness, and interpret I Timothy 3:2 as saying church officials *must* be married, and possibly even must have children! By that standard, both alphas and omegas could validly be pastors, and might even be more common than betas. Churches with Catholic-style priesthoods, though, probably have only beta priests.
Starting with the Enlightenment, there is probably a Protestant schism in which some churches want to enfranchise omegas, some churches favor the status quo of omega disenfranchisement, and some churches want to disenfranchise alphas too! (For being equally irrational.)
I imagine that not only do Mormons still practice polygamy (possibly with an alpha-only priesthood), there are other right-wing churches that do the same. "Complex marriage" may have survived the end of the Oneida colony, for instance.
In the absence of Scripture explicitly stating otherwise, some churches will probably argue that alpha women are men and omega men are women. The number of churches arguing this will initially *increase*, not decrease, as some of them learn more about biology (for instance, with cryptic male fish). Multiple types of sexual conservatives are likely, with some accepting only male-female pairs, some only alpha-omega and double-beta pairs, and some requiring that pairings be both male-female and alpha-omega (or double-beta).
Following the decline of Calvinism, most conservative churches do accept female alphas and male omegas, with some restrictions.
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