I have a feeling this plot point will make an appearance, probably towards the end of the series. A Mr. and Mrs. Smith type of arc.

That reminds me of Assassin's Creed Black Flag. There's a subquest where a Templar and an Assassin are in love, and you end up killing one, with the weirdest confession I saw. It went something like "I would've died happily if I got to kill you first".