Unless the deals completely revert to Marvel after the trilogy is over, the SM deal was a poor one on their end. Besides all the stuff I have previously mentioned, Marvel can't even use Spidey for promos for their movies in the theater or home release. They also can't use them his footage in the new logo.
The deal was fine. Not only did they use Spidey in the final Civil War trailer, they secured a character that was on the verge of getting a horrible forced cinematic universe.
Every time you doubt the Spider-Man deal remember that the alternative was Spider-Man being a member of the Sinister Six and teaming up with a British Sandman to punch a dinosaur. And if you think that sounds totally fucking awesome keep in mind that Avi Arad would have fucked it up.