or try to do a Frankenstein with the story so it fits the story of past movies
They already setup how they could do this in Into the Spider-Verse.
Peter gets teleported to a parallel reality where the MCU never happened; no Cap, no Iron Man, no SHIELD, and Peter has to navigate a new world dominated by Oscorp. The Peter of this world never became Spider-Man, maybe because his Uncle didn't die or died for another reason.
Our Peter teams up with New Peter and teaches him to be Spider-Man. They end up working together to foil Norman Osborne's attempts to cross the dimensional barriers and steal technology or something from other realities, but MCU Peter is trapped in this new reality. He adopts the name Ben Reilly, and passes the mantle of Spider-Man to his doppleganger while he tries to establish a new life for himself in this world. Subsequent movies focus on "new" Peter, and you've got a setup for future Clone Saga-type shenanigans.
Or, replace New Peter with Miles and basically do a live-action version of ITSV, but I don't think that's a good idea when you've got Holland.
I hope that everything goes the way it should and S-M stays in the MCU, but Sony is hardly written into a corner without doing a complete reboot of the character.