I think that this is more like what happened in Quantum Leap. Sam "leaps" into the body of Lee Harvey Oswald just before the assassination of JFK takes place. Sam does his thing and everything goes back to normal. Except...not quite. Oswald managed to hitch a ride with Sam and, over the course of the season, begins to fight and take over Sam's brain.
In the case of Spider-Man, there could still be a little bit of Peter left that could, until the plotline starts waning, be building up enough strength to take on Otto and a big battle royale could ensue inside Spidey's mind. And because comic books are comic books, Peter will win and Otto will be completely vanquished...perhaps with the help of Doctor Strange.