A/N spoilers for 4x11 The Depths, enjoy!
As she said she would grant him amnesty, but she would not forget. How could one forget such hurtful words? Even those said in a situation like theirs, would not be forgotten soon. She knew if he did not had thought about these things prior to their mission, he would not have said them. As much as the comment hurt she was sure that he did not mean to include Ashley in there. She was convinced that that was added as an extra kick to hurt her during his withdrawal. He knew better than to think that her daughter had not meant the world to her, did he not?
Even if he had not meant what he said it had opened her yet again to doubts that what he said was true. Not just about Ashley, but all of it. Did she really see life as a game of chess? That the people she worked with and cared about were expendable?
She was well aware that she did not connect with her staff the same as before, but did he forget that she only just returned? For him there was not a gap of decades that separated then from now, just a matter of months. She had history seen repeated. Seen mistakes be made all over again, all without interfering. He would never know how hard it was to stand by and know what will happen and still let it happen. How much it saddened her not to interfere with events that would have saved so many from suffering. Not to protect the ones she cared about from hurt.
She might not been as close to those she knew during the first time she lived it, this time she had the knowledge that they suffered and could only watch from a distance. All the while, remembering and reliving it as well as see the people around her suffer and know at times that it would become worse. As she told him, it was not something she wished on her worst enemy. He did not know how hard it was to carry that around.
On top off this all, it hurts that he does not thrust her. Though his words were spoken in moments of withdrawal and anger, they told her that they were bothering him. She thought he knew her well enough by now to know she cares about those around her. That she does not take people's lives for granted. That she often would rather die herself than see those around her suffer. And that she would never have forced him to join the Sanctuary when she paid for his education. She cannot deny that she hoped he would join, but if he had not accepted her offer she would not have hold him prisoner. He is free to make his own choices, as is everyone else. She is not God, nor does she play God. That he thinks so, is what hurts the most.