
James Gunn leaving the MCU most definitely affected the future of the Guardians of the Galaxy, but it also likely changed Marvel Studios' plans for the next two Avengers films, Doomsday and Secret Wars. Gunn was an integral writer and director for Marvel Studios with his Guardians of the Galaxy movies, so after he left to start an interconnected franchise with DC Studios, which will include 14 Marvel actors, Marvel Studios likely had to redirect its course for the future.
After Gunn became the co-CEO of DC Studios, he became exclusively tied to that brand, meaning that he would no longer be involved with projects at Marvel Studios. It is no secret that the Guardians of the Galaxy trilogy writer and director formed close bonds with the stars of those movies (such as Chris Pratt, Zoe Saldana, Dave Bautista, Karen Gillan, Bradley Cooper, etc.). After Gunn was fired by Marvel Studios, those actors openly signed a letter to have Gunn be brought back for Guardians of the Galaxy Vol. 3.

Some Guardians actors, such as Bautista, already publicly stated that they would not return to the franchise under any circumstances. While appearing on The Tonight Show Starring Jimmy Fallon, Bautista pointed out that his character, Drax, "had the perfect exit" in Guardians of the Galaxy 3, and that "he would never sign up for another job as Drax just to get a paycheck:"
"It's the perfect exit. We all had those perfect character arcs and such a storybook ending. I constantly relate it to the way I ended my wrestling career. I ended it on a storybook note. And I would never go back and tarnish that. And it's the same with this. With Drax, I just got to end the perfect way. And I would never sign up for another job as Drax just to get a paycheck. I would tarnish that, and I won't do it."
If Gunn had stayed on with Marvel Studios, the direction Marvel Studios would have taken with characters in the Guardians movies likely would have been different. Instead of Guardians 3 being an ending for some of those characters, they probably would have played an integral role in Avengers: Doomsday and Avengers: Secret Wars, potentially even being leaders of the Avengers in those films.
However, because of Gunn's departure, Marvel Studios probably had to change course and make other characters in the universe more prominent since some of the Guardians wouldn't be available.
At the end of the day, Avengers: Doomsday and Avengers: Secret Wars may have initially looked a lot different when Marvel Studios first began planning for them and creating storyboards.
Similar to Bautista, Zoe Saldana also recently confirmed that her time in the MCU is now over. Speaking to Variety, Saldana rejoiced in the time she had to play Gamora, but didn't want the character to be left alone. Instead, she was only speaking of her as an actress saying goodbye to the MCU, hoping that Gamora would be recast:
"I think my role was great. My journey and partnership were memorable and so rewarding... I keep saying this time and time again — I can’t wait to see what’s next for Gamora. I hope they’re not done with her, and I hope a woman of color or a woman with special needs can take on the role next. That would be incredible."
Once again, it is hard to imagine that Saldana would not continue to play Gamora in at least the two upcoming Avengers films if Gunn were still attached to Marvel Studios.
How the MCU Changed After James Gunn Was Fired

It is important to mention that Marvel Studios already had to make major changes to its plans a few years ago when James Gunn was fired. Before Guardians of the Galaxy Vol. 3 went into production, Marvel Studios announced that they fired Gunn due to tweets he made many years prior.
Before the company fired Gunn, the Guardians writer and director revealed in a Facebook live video that his films would "set up the next 10 to 20 years of Marvel movies:"
"('Guardians of the Galaxy Vol. 3' will) set up the next 10 to 20 years of Marvel movies [and] really expand the cosmic universe."
In another instance (this time in an interview with The Wrap), Gunn even revealed that he was consulted for other MCU movies that he did not write or direct:
"I was consulting on everything. I was consulting on all the Marvel movies. Kevin would send me the script for ‘Spider-Man’ and I’d give my notes. He’d send me the script for ‘Doctor Strange,’ ‘Captain Marvel,’ and I’d give notes on all of those scripts."
So, it is clear that Gunn was being set up to take over an executive role at Marvel Studios that would have entailed him leading the cosmic side of the MCU. However, after Gunn was fired, Marvel Studios immediately changed plans. Gunn wasn't included in as much because, for a couple of years, the franchise had to move forward without him.
If he had not been fired and had started a full cosmic side of the MCU that would have lasted for 10 or 20 years, the Guardians would have likely been an even bigger staple of the MCU than they already are. The team could have even become as big and as important as the Avengers are in the franchise.
So, it is almost a guarantee that Marvel Studios had to drastically change its plans after Gunn started his DC franchise. Those changes will undoubtedly be felt for years to come, but it is clear that they definitely affected Avengers: Doomsday and Avengers: Secret Wars.