The last thing Wanda expected to feel after this revelation was sympathy, but it was difficult to listen to actual honesty from Tony and not feel at least the stirrings of compassion. It was a small relief to hear that there was nothing nefarious that motivated him. Only love (which was perhaps nefarious in it's own way). It was enough in her mind to explain even that still unanswered billion dollar question.
Wanda might despise his choice but she would never begrudge his loving someone. Even Mystique. Love was completely illogical and didn't end just because you learned the truth about someone. She couldn't blame him for loving a terrorist any more than she could blame herself for seeing a demon or still caring for her brother in spite of everything. Love could make a total fool of anyone, which Wanda knew all too well. It was the reason she'd stayed when he'd told her to and was still sitting here beside Tony, wordlessly forgiving him. It was the reason she reached over to take his hand while she banished her doubts about his loyalties. He wasn't under mind-control or willfully aiding the enemy, he was just an idiot in love. Wanda could believe that.
What she couldn't believe in was Mystique's innocence. Tony thought he could fix anything and maybe he thought he could change Mystique. But even if Mystique's affections for Tony were real (and Wanda couldn't believe that either), it was impossible that she was working all this time for S.H.I.E.L.D. without being a spy. She'd just made her feelings about they country pretty clear, and they weren't nice ones. That she would willingly serve it again just didn't make sense. Tony had to at least realize that.
"Tony," she began quietly, "I’ve known that woman almost my entire life. I just don’t trust her. I'm sorry. But I do trust you. And I want to think that you knew what you were doing here, that you weren’t deliberately putting us in danger. So if you didn’t think you needed to tell the Avengers, then fine, that’s your choice. I won’t tell Steve unless she- unless it becomes necessary. But Nick doesn’t know. He doesn’t know that he might have a spy in S.H.I.E.L.D. And he deserves to know. Think what my father could do with the kind of information he could get from S.H.I.E.L.D."