This all works for me too and actually I'm not sure if he'd assume that right off the bat - he'd probably initially assume that she just fell under the sway of Assassin lies and falsehoods and her allegiances shifted, not that they're Actually Involved. If that came up right after they get done running like hell it'd probably be all kinds of hilarious. I.E., one of them gets close to the other to check on injuries and it's a moment of tenderness and he takes one look and goes OH HELL NO or something similar.

That thought amuses me. Asscreed could actually stand to gain something through an approval system honestly.