The later recons obscure this, but Halo’s Human-Covenant war is absolutely a mythologization (not 1:1 allegory) of the ascendant Church and its contention with the Pharisees.
John, who is both savior and apostle, is the exceptional seed of the creator race which the Covenant worships. He comes to fulfill what the Forerunners built while thwarting the misguided zeal of the (old) Covenant to make way for the new reign.
The arbiter being chief persecutor of “heretics” only to then join them after a conversion is, as the quoted post suggests, a strong parallel with St. Paul.
The Arbiter is an allegory for St. Paul btw.