I found nothing confusing about JOURNEYMAN, DR Jennifer.
Dan's wife basically wanted to go back to their old life, and Dan, of course, said that would never happen.
He also as much as said that he wanted to stay together, but that if his time traveling was going to be a burden to her, he could understand her feelings, but that HE felt he was contributing something major to the world, making a difference, and really wasn't eager to give that up even if he could (she was urging him to try medication to induce sleep that might help control the time traveling.)
She had mentioned earlier that she wanted to see him disappear but had missed him the last time it happened due to her meddlesome sister (who REALLY wore on my last nerve.) Dan roused her out of sleep as he was vanishing, and she got to see it for the first time.
The camera zooming in on her pupil I didn't read anything symbolic into. Rather, it was just a different way of "fading to black."