A high level explanation
I think taking this movie literally is both making it too easy and too complicated. On one hand it's too easy because it doesn't require an awful lot of imagination. On the other hand, it's very complicated because you end up with "weird" stuff that has to be explained (like parallel universes, force fields, guest house windows with weird properties, etc).
I like to think of the movie as representing a therapy session. They were, after all, "sent" there by the therapist. I like to think that the different personalities in the movie represent different personalities within Ethan and Sophie. The therapy session makes these personalities come out, at first just for a few moments but later on more and more. However, only one personality per person can walk out the door at the end of the session.
So my interpretation is that they went to a therapy session, talked about their problems and the therapist brought out different parts of their personalities, and then finally they went home. Ethan was probably quite the same after the session, except that he had learned which qualities Sophie was missing in him (the things she liked about Ethan2). Sophie had done the same, which is displayed at the very end when she suggest cooking bacon for breakfast, something she wasn't fond of before but which was one of the things that Ethan liked about Sophie2. Ethans shocked stare at the end of the movie simply displays his surprise that the therapy went so well, and that Sophie had actually changed.
I think it doesn't really matter if Sophie at the end is Sophie1 or Sophie2, because they're not that different anyway. Ethan2 was more drastically different than Ethan1, so his part of Ethans personality had to disappear during the therapy session, which is why he was killed by the "force field". I take it that the therapist and/or Sophie made it clear to Ethan that he should try to avoid displaying the Ethan2 -part of his personality.