The passage doesn't apply to same-sex marriage at all, because it establishes a relationship of gender-based subordination (though with beneficent concessions, of course). The idea of two Christs or two churches just over-extends the symbolism of this passage into someplace it was never fit to go.

I'm not sure how literally the passage is taken anyways. Most of the Orthodox people I know are Coptic, and that's as much a matriarchy as any culture I've encountered, despite the all-male clergy.