She’s disappointed in the both of them and makes her choice in choosing Henry for the time being.
This is totally understandable. Emma really can’t focus on romance at the moment because her priority is saving Henry. But like Hook hinted, once they get back to Storybrooke, she will have to make a decision.
And that section, you know what it’s called guys?
Emma’s Choice
It also says:
“Killian is fully aware that she’s not a prize to be won, he believes that she is his savior, he’s a better man because of her – the man of honor he used to be. But he’ll need an answer at some point, if only to know if he can still allow himself to hope.”