As I write this, it is mid-August and John Byrne's reboot of the wall-crawler is about six weeks away. There has been some consternation emanating from Spidey fandom-at-large about just what big John is planning to do to Peter Parker and his universe. No one is going so far as to fear the resurrection of Uncle Ben but, other than that, any fear goes. So far, though, the only change I've heard about is the one where Doctor Otto Octavius is a professor at Empire State University. It is his experiment in radioactivity which simultaneously creates Dr. Octopus and Spider-Man.
Some people dislike the sound of even that... and I sympathize with the hard-liner who likes to keep his continuity intact. (After all, it drives me crazy when the Puma still remembers Spidey's identity even though the Black Crow previously took that memory away or that Spidey doesn't remember the Frankenstein Monster when he teamed up with him once before.) But, when it comes to this Spidey/Doc Ock origin connection, when Byrne finally presents it... it won't even be the first time it has been done.
In 1994, a collection of short stories entitled The Ultimate Spider-Man came out from Berkeley Books under the imprint of Marvel Comics and Byron Preiss Multimedia. It featured prose work by various comic book and science fiction writers (including our own Keith R.A. DeCandido), telling Spidey tales from throughout the web-slinger's career. The collection begins with a novella by Peter David and Spidey co-creator Stan Lee which re-tells the origin of our hero. In that tale, Doctor Octavius is a professor at ESU and his experiment in radioactivity goes awry, bringing about Spider-Man, Doc Ock, and the good Doctor's obsessive hatred of the wall-crawler. Not the origin to which we have become accustomed but still a heck of a good read. One of the best stories in the book. And, sometimes, continuity must just go by the wayside in the service of a worthwhile tale to tell.
So, don't be concerned about Byrne linking Spidey and Ock. Stan and Peter David already did it before. My advice would be to sit back and enjoy the whole ride, no matter what changes Byrne cooks up. Personally, I hope he shakes things up something fierce. We haven't had fun like that since the clone saga.