if they really plan to make the Civil War mini-series into a movie or set of movies then they will need to get SM into the mix. I’d be surprised if they don’t also try to deal on X-men since they play a big part in the storyline as well.
Civil War is way too big of a story to be crammed into one movie. And Marvel’s moving steadily towards the two part Infinity Wars conclusion to Phase 3.
So I’m guessing in the Cap Civil War movie they stick to the concept from the comics and condense it down considerably so it doesn’t require Spidey.
At the same time the targets of the “Registration Act” can be the Inhumans, which were just introduced in Agents of SHIELD and may play a role (Scarlett Witch and Quicksilver possibly being Inhumans) in Age of Ultron.