That's my predication too
A high-profile win for the Accords. A vigilante coming out as a registered hero. A legitimate reason for the Daily Bugle to be wary of Spider-Man. And Peter gets the perks of working with Tony and getting a cool costume upgrade from his makeshift outfit
I never read the Civil War comics, but Spider-Man was a wild-card during them; he had real reasons to join both sides and was torn on which one to be a part of.
I like your suggestion; Peter signing with Tony's side as it really has no downsides for Spider-Man. No worries about being bad-mouthed by the press, can get a better costume, can work with his hero (both in the comics and the TV shows, he respects Iron Man and Captain America a lot), and will be reconsigned as a hero by the world.
I just wonder how they will use Spider-Man in the film.....I guess it might work like this:
-Opens with the battle that pushes the General from the MCU Hulk film to pitch the Registration Act
-Steve/Cap gets wind of this and tries to get Winter Solder/Bucky away as if he is registered, he will face a lot of trouble
-Tony/Iron Man and the other Avengers talk about signing up for the Registration Act, as they have a real reason to do so (people see them as the reason why NY and the world faced such destruction in both Avengers films).
-Tony, War Machine, Black Widow, Vision and others agree to sign up for the act but half of the Avengers (Falcom, Cap, Hawkeye, ect) refuse
-This leads to the films core conflict taking stage and in-between it all is Cap & Bucky bonding, being closer friends again
-Spider-Man hears about this and other superheroes in the Marvel Cinematic Universe being on different sides (reference Agents of Shield, Daredevil, Jessica Jones, upcoming Iron Fist and Luke Cage shows, Doctor Strange, ect).
-Iron Man pays a visit to Spider-Man, telling him the benefits of signing up for the act (mirroring your statements)
-Spider-Man initially agrees on Tony's offer and joins team Iron Man
-Big fights happen and Spider-Man sees Captain America's view point (even having a talk with him)
-Spider-Man makes a choice either being part of the fight or leaving the fight
-Movies events continue, with it ending having Tony talking with Peter Parker about joining the New Avengers