Like I said in the Far From Home thread, the studios and the fans have different definitions of what the Marvel Cinematic Universe is. To the studios, it's a branding thing, movies made or produced (or co-produced) by Marvel Studios. To the fans, the Marvel Cinematic Universe encompasses the movies, the ABC shows, the Netflix shows, the young adult shows, the one shots and the internet content. Since Sony had already confirmed that they're going to continue on from the cliffhanger established in Far From Home, by the fans definition of the term, the spider movies moving forward will still be a part of the Marvel Cinematic Universe. Sony's Universe of Marvel characters will obviously take place on the same storytelling world as the Marvel Cinematic Universe, the Netflix shows and the rest. The connection will just probably be one way, as with the rest.
And for that matter, we don't know that Marvel won't be willing to share characters or concepts. Both sides say the split was amicable. Kevin Feige will still be in the loop and will offer notes as he says he has for every Marvel project produced by another studio. At one point, even before the character sharing agreement, Sony and Marvel were willing to stick Avengers tower in Amazing Spider-Man 2 and the Oscorp tower in The Avengers, they just didn't have time to render those buildings into those respective movies. I think it entirely possible that the doomsday scenarios being thrown out there by fans are extremely premature.