He did register, and people knew his identity THEN...
But it has been forgotten...
Man, I hope Marvel can really give us a good explanation... 
Well lets use process of elimination/logical deduction to come up with the way this would most likely work.
1)Nobody remembers his true identity
2)He did publicly unmask
3)Magic has removed public memory and record of his identity
It seems most logical that even if he did register, that when Mephisto removed the memory of who Spider-Man was, that this also removed any recorded documents or files about his identity. His alter ego is the only known name (Spider-Man) while any file showing him as registered, would only show him as Spider-Man. No picture of his face, no written statement about his real name. So he agreed to fight on the registration side (Spidey Armor # 2) but his real identity still remains unknown. That still allows him to renege on his word with joining the registration, while still keeping his identity secret. Honestly I think matters such as this are easy to resolve based on the use of magic.
For instance, Peter worked with Tony Stark as an assistant (or more or less as a replacement to Rhodey). Tony employs Peter, but not because he is Spider-Man...but because he recognizes Peter as an intelligent mind. Peter still worked for Tony and remembers this, but he never divulges any information about his identity. So he worked for Tony Stark but once he buts heads with him, he changes his mind. So Tony is most likely aware of Peter and Spider-Man, but not that they are one and the same. This still allows for Peter to disagree with him in the negative zone, but he does so soley as Peter Parker the assistant, not Peter Parker Spider-Man.
I think most readers major problems, is the fact that the back issues can't possibly reflect these changes, but in reality they don't have to. They all happened as they happened originally (MJ married, Harry dead and all) but at the point where he barters with Mephisto, the time frame changes and continues from that point as if those past events occured differently. But it does not change the fact that they occured. It's sort of like in Back to the Future and the Clayton Ravine. Before Doc and Marty went back, Clara fell into the gorge and as a result of her death, it was named after her. When they saved her, it altered things from that point, but the event still occured because Doc and Marty understood that she should have died. The only difference in this juxtaposition, is that Mephisto extended this memory lapse to the person who existed outside of the anamoly as well as those within. But the same basic ideas applied.
I am sure that all higher order beings of the Marvel U are aware of this, such as The Watcher (who is aware of the 616, 1602, What If etc) is aware of it. Or another example within Marvel continuity would be Bishop. When Professor X was killed by his son, it altered the path of history at that point, but it did not undo history as it was, if that makes sense. Bishop was still aware of how things went before, even though he existed in a reality where the things he remembered, did not come to fruition from the point of the accidental assassination. Another example would be House of M, where this time, Wolverine remained aware of the difference. So everything Wolverine knew had happened in continuity, but from the point of House of M, they did not continue that way. These continuity resolves, though convoluted, have been done before and some what frequently. They do not occur despite the past, but rather occur in spite of the past. We can't have a reality where Spider-Man's marriage was dissolved, if he were never married at some point in continuity. So your back issues still matter.
t:
