In her heart, she knew he was right. He was, after all, almost always right. And she knew he really didn't have an awful lot of choices of what to do. It just felt like she was the one stuck because of it. She hadn't created the other him. It wasn't her fault there was an odd man out. Why did she have to suffer because of it? Again. Selfish.
But she also felt badly for the not-quite-Time Lord. He was completely alone, save her and her mum and Pete. He'd been left in a world he knew little about, except for what the Doctor knew from living there before. He was left with no possessions of his own and no one to turn to except a woman who he knew didn't really want him there. Or, more so, didn't want to be there herself. And all while knowing the person he should have been closest to had sent him packing.
It was hard, knowing what she needed to do, especially when she looked into those pained brown eyes that were so much older than the rest of him. The last him had nice eyes. And so did the newer one. But none could grab her heart like this one did. Tenderly, she lifted his hand to her lips, kissing his fingers gently before shaking her head. "You've been hurt. You've seen people get hurt. It's understandable." She hesitated, afraid of overstepping her boundaries. But if she couldn't, who could? "But you've got to learn that you can't do everything on your own. You've always moved on. You moved on without me, without Gallifrey, without everything you've known. And you've survived. And it was hard and I know it had to hurt, but you have because you're a survivor. It's who you are."