I suspected this might be an issue when I started my game, so I started out by setting two ground rules: 1, Harry died at Bianca's party. 2, It is a year after that event. From there, everyone else contributed as normal. Setting such a major event as a founding "truth" to the campaign allowed everyone to accept later changes as they came, since it wasn't assumed to be the exact world of the books.
For my part, I've only included three cannon characters, and only in bit parts.
Thomas showed up at a vampire party as the House Raith representative, but in a world where he failed to save Harry's life, he's a bitter ass. The players got to outshine him. They loved it.
Morgan appeared once to stress The Laws to our budding magus. He was basically all *intimidate, spell out the letter of the law, threaten, leave*. It was enough to warrant no further Council intervention.
Finally I had Maeve show up at a ball. The one player who was ballsy enough to introduce himself got snarked at and insulted (as politely as possible)-- as you'd expect from someone of her stature. He snarked back of course, in courtly fashion, and everyone got a laugh.
These visits cement to them that, yes, it's the same world with its own internal consistency. The book characters also don't stick around after serving this purpose, which allowes them to get out of the players' way and let their characters be the awesome ones.
YMMV, but it's worked really well for me and my table.