We have completely no idea what Ancient timeframes are like or what 'long' would be for them, but it's pretty clear they were together for a while. They have a child! Who is at least be fairly grown by the time of that scene; my best guess says maybe he's the Ancient equivalent of, like, eight years old. Even on normal human scales... holy crap, imagine learning eight years after your son was born that your partner's only been using both you and him as tools and test subjects.

And if you still think she could be totally cool... I assume you're picturing yourself as Athena in this situation, and not as Lahabrea or, even worse, Erich.