Just my two cents.
I don't think they're going back to their own timelines. I think they're stuck where they are, and I think Wells did this because of some dastardly scheme Tempus came up with and this radical idea was the only way to "fix" the problem, whatever it is. It's a little tragic for both Loises, less so for Clark, but if it preserves Utopia, what's the problem?
It isn't neat, it isn't pretty, but unless Sue has some dynamite plot twist coming up, I don't see any other way to end this epic tragedy. After all, if you redirect your past, you risk bending your future so far away that you can't get back to it.
