I know my weighty opinions/recommendations will be worth nothing after this admission but I was reading comics occasionally during the Clone Saga (being in school etc) and was totally taken in by the whole thing. I haven't read the thing end-to-end but the whole wheels-within-wheels-within-even-more-wheels-and-no-end-in-sight thing actually appealed greatly to me.
Actually, I quite enjoyed the entire story myself. And I did read it from beginning to end. I had no problem with Ben being the original as so many other fans did. At the point where the supposed switch took place, either one was as real as the other. So all the stories I read after that were still valid and still in continuity. We were reading Spider-Man and he was the only one during all that time.
And yeah, I did read the book before that. I started with #100, the beginning of the story where Peter got four extra arms.
But I really think that if they had not said Ben was the real one, no one would have had a problem with Peter handing off his identity to Ben when he and MJ went off to Seattle to live a normal life and raise their baby. Allow Ben to take over the Parker ID as well, so that even people who knew his identity could be fooled into not knowing there was a switch. People like Daredevil, Wolverine, Black Cat and even Norman and Harry Osborn if they were brought back a bit different than they have been. Plus, it would let Ben return to the Daily Bugle.
The new Peter could just tell people that MJ left him for his cousin Ben. Something that would have made them give the real Peter a bit of space to get over. Allowing the new Peter to get up to speed on all that he had missed when he was away. And viola! You would have had a single Peter as Spider-Man working at the Daily Bugle, one that would have never been married.
The old fans would know that Peter and MJ were just fine living off-panel, no deals with demons, so they would have handled it without a real uproar. And editors could just start ignoring there was a switch after a while, once Peter(Ben) settled in. And after that, for all intents and purposes, he's Peter. Period.