Killian loves Emma so selflessly and has and always will fight for her well being and happiness. He has literally gone to the end of the world and time for her and even traded his own home for her thinking he would never even see it again. He has never let her down and always came back for her/to her.
I feel that his happy ending does not even include himself with her. He would be content if Emma is happy and safe. She literally *IS* his happy ending.