Survival had been the key aspect in Emma's life for so long that it was largely all she knew how to do. And then Storybrooke happened, and helping people became something she felt innately drawn to doing, she had a job to do, and saving the town seemed to be what she was always meant to do. Her magic, her birth, her parents -they all joined in one key aspect; Emma was a source of goodness.
That was what she was being faced with day in and day out.
The fact that she'd turned so sideways on that, that she'd twisted herself inside out and done things she could've never imagined before, it wasn't sitting well with her at that point. Killian might forgive her for turning him into the one thing he hated the most in the world, and maybe the people here would forgive her eventually -if they stayed long enough to remember at all, but Emma would take longer to move past it.
"I can't make excuses, I can't fall back on that." It didn't make her pull away though, his arms were comforting and Emma had forced herself to stay away for so long, sure that if she could do those things to those people, she could hurt Jefferson just the same.