Captain America: Civil War is a pivotal movie in the whole Infinity Saga. The movie sets up the future events while focusing on the current Avengers team and their differences. However, the movie had slight differences from the comic. Instead of Superhero Registration Act, the movie used Sokovia Accords as a way to regulate the superheroes under the UN. Steve Rogers (Captain America) was against it but Tony Stark (Iron Man) was in favor of it. Although this was the start of the initial conflict, the fight became more personal in the third act. But there was a moment when the movie might have had an alternate ending that would have seen Avengers reassembling.
The movie’s original ending sees Iron Man initial patching things up with Captain when he gets to know that Bucky Barnes was framed by Baron Zemo. However, things started heating up again when Tony Stark got to know that the Winter Soldier killed his parents. And that Steve Rogers purposefully kept it a secret. This resulted in an intense fight between Iron Man and Captain. This also gave a chance for Thanos (Josh Brolin) to attack Earth while the heroes were scattered around the globe.
The Story of Marvel Studios: The Making of the Marvel Cinematic Universe (via ComicBook) revealed that the movie could have had a different ending. The Marvel Creative Committee wanted to change the ending of the movie. Instead of the original ending in the movie where the team was still broken up, they wanted to reassemble the team. The committee wanted the team to fight Baron Zemo and his team of super soldiers in the final act.
This was also the same time when the Russo brothers wanted to quit the project due to this alternate ending. However, Marvel boss Kevin Feige sided with the directors and talked to Disney Chairman Alan Horn about the alternate ending. Fortunately, everyone sided with the directors.
This particular decision had major ramifications in the future. Not only did the Russo brothers stay for directing Captain America: Civil War but also helmed other projects in Infinity Saga. Also, it led to the defunctioning of the Marvel Creative Committee. Also, the canon-ending of the movie sets up the MCU for major events with massive impact.
If the alternate ending would have made its way into the movie, it would have been underwhelming for the audience. To watch the conflict between Avengers only for them to reassemble again for a final showdown fight would have felt the same old same old. Also, if the Russo brothers would have left the project, Marvel would have had to change the future of the Infinity Saga. They might have ended up with a very different and less successful finale for the Saga.