As a new-52 Superman fan who's upset that they are killing him off and replacing him with SuperDad, I'm not sure how saying new-52 Superman was Kon-El all along would be throwing me a bone. It'd be more like flipping me the bird.
To begin with, this Superman directly interacted with Kon-El in several of the crossover events. They were both in the same place at the same time.
So, I guess they'd be saying he is the Kon-El from the pre-Flashpoint continuity. Um, so who does that make the new52 Kon-El? Krypto? But wait, there's already a new52 Krypto, so we'll say new52 Krypto was, um, Jimmy Olson, and then new52 Jimmy Olson can be the pretzel guy from the pre-Flashpoint continuity, and then... See how stupid this is?
Also, isn't Kon-El 50% a clone of Superman and 50% a clone of Lex Luthor? DC Comics is going to try to tell us that thry've been feeding us Lex Luthor's genetic son as Superman the last five years? Or, oh, hey, wasn't one version of Kon-El the son of Lois and Clark from the future, who's name was... Jon? *Head thud*. If they try to tell is that Superman of the last five years was a grown up version of that annoying 10 year kld superhero kid, I am going to lose it.
Editorial would have to be actively trying to run the line into the ground or trying to flip a certain segment of their fan base the bird to try to pull something like that.
If they are determined to never bring the new52 Superman back, just say he was a fragment of Superman and merge his life and memories into SuperDad so that we get one unfiied version of Superman who remembers every adventure of every comic book with a Superman from 1986 to the present. At least that'd be something. Better than a Superman who doesn't remember any of the comics we've bought the last five years.