According to showrunner Marlene King, she will. When a fan asked Marlene on Twitter if, in Season 3, Emily will have another love, Marlene tweeted, “She will eventually move on from her loss.”
We know there will be a new male love interest for one of the girls, but we doubt that Emily will suddenly start liking boys. Her relationship with Maya seemed to cement Emily’s proclivity towards girls. How Emily will “move on” remains to be seen!