Exactly. She actually said "I trust him" outloud, which is a HUGE deal to Emma, and IMHO, as important as love for her. For example, she loved Neal, but I'm not sure she could really trust him any more. She included Hook in their meetings, waiting for him to the point that Charming actually had to tell her that stopping Zelena was the priority.
And that makes me ask, did Charming know the details of Hook's curse? He knew about it in the hospital but when Emma said Zelena took her magic he didn't seem to know how it could've happened.
She was really scared and I think it was one of the moments when we saw her being the most vulnerable. When she says "Hook, I can't..." she was looking at the floor and stuttering. I don't think we've ever seen Emma stutter other that in that scene.