3) "I'm sorry about how I reacted; even though I know on the level of rational probabilities that it's extremely unlikely you meant to hurt my feelings, I'm still working on getting my brain to alieve that and not just believe it."

Even as a rationalist, this line is a bit of a turnoff. If both spouses like this kind of phrasing, that's great, but that's an issue of shared culture, not inherent superiority of rationality. I preferred option 2.

Edit: more accurately, I think real rationalism promotes good relationships, but the Less Wrong lexicon is not inherently helpful.