Well, here's how I think that they could retcon the Spidey thing:
Reed created a clone of Spidey when he first joined the Pro-registration, just in case he decided to turn on them, and he's stasted away somewhere. Some time later, the clone awakens and thinks he's Spidey, gets a costume, and starts swinging around town. Later, someone sees the other Spidey and Pete together, and everyone assumes that Pete isn't Spidey, and he gets arrested for impersonating a superhero.
Yeah, kinda crappy.:sweat: