I've just ruled that in my game, everything up to Small Favour has happened, with one or two small changes to canon, like
one of my players having known Michael and due to an encounter they both had together, Michael chose to hand the sword over to him rather than leave it in Harry's care
(Small Favour Spoiler).
From the end of Small Favour onward, I've told my players, things won't be happening as they have in the books. Turn Coat may happen, but Changes, probably not so much.
I'm running my campaign as though each story arc or scenario is a book in a series. So when we play we can focus entirely on our Boston, and not worry about Chicago. Anything major that happens that I want to incorporate I can alter or have mentioned in the background without it being an issue in-game, since the odds of even the events of Turn Coat having an effect on a 3-4 day period out of an entire period of 6-9 months are extremely low.
I don't need to kill Harry, just ignore him. He's not the only one who has evil to stop.