Thomas, I really don't think this is your fault. I don't think it's necessarily a matter of signals. You and Scarlett went through something terribly fucked up together. She probably feels the need to cling to you more than she knows is actually possible, so she's expressing it in ways that she feels will make her closer to you. It's not something to hate yourself over, my darling. It just goes to show how much you mean to her now. As long as you two can build that into a healthy relationship, then there's nothing to feel bad about.

I'm so sorry you feel ick though, my love. You don't deserve to have things make you feel like that, and I feel awful that the Templar have put you in a position like this.