The idea of villains solely being bad guys who only do bad things is a common trope, but also overplayed and unrealistic. Even movie villains, MCU included, aren't always 100 percent bad. Sometimes they do bad things but have a good reason or have no other choice. The best MCU villains are morally complex people whose actions are often understandable.
As a result, there were many instances when various MCU villains did something that can be considered a good deed. Whatever their reason for this was, it proves that even villains are only human (and sometimes aliens), and as such, they're bound to make mistakes in some cases.
Red Skull: Guarding The Soul Stone
To be fair, it seems like Red Skull didn't have any other choice than to guard the Stone. That doesn't change the fact that the Red Skull the heroes met on Vormir was very different from Captain America's iconic enemy in the Captain's first solo movie. Guarding the Soul Stone is an important task since it could do a lot of damage if it fell in the wrong hands - as Thanos demonstrated.
Ghost: No Longer Fighting The Heroes
Ghost is one of the villains who is ultimately more sympathetic than villainous. The story reveals that she got her powers in an accident and it brought her nothing but torment. Ghost just wants to figure out how to get better and live in peace. Once Janet van Dyne offers her the chance to do just that, Ghost is quick to take the offer and no longer attacks the heroes.
Vulture: Taking Care Of His Family
Michael Keaton's Adrian Toomes is one of the more relatable villains in the MCU. He's presented as a hard-working man who turns to crime when others rob him of his opportunity to do honest work.
Toomes's greatest desire is to take care of his wife and daughter and he seems more level-headed and civil than most MCU villains. He's even willing to let go of his grudge against Spider-Man to ensure that his daughter Liz is happy since she likes Peter.
Yon-Rogg: Saving Carol's Life (Presumably) And Training Her
Yon-Rogg is one of the more confusing villains. He originally poses as the good guy but it's revealed later on that he's the one responsible for killing the original Mar-Vell. Despite his many bad character traits, nothing is black and white with Yon-Rogg. He does train Carol to be a better fighter which later comes in handy.
And he also presumably saved her life when she got her powers. If he just let her lie there, who knows whether Carol would have survived. It's true that his motivations were far from pure but that doesn't change the facts he was still originally helpful to Carol.
Thanos: Saving Gamora When She Was Little
There's no denying that Thanos was a horrible father to Gamora and Nebula. He tormented Nebula, tortured her, and he killed Gamora on Vormir to get the Soul Stone. On the other hand, Thanos could have easily let little Gamora die alongside all her people when he attacked her planet. Instead, he gave her a chance to live and meet the team who would later become her new family - the Guardians of the Galaxy.
Loki: Helping Thor
Loki and Thor were both brothers, enemies, and friends (sometimes). Loki stood against Thor most of the time but when a mutual, more powerful enemy came along, they joined forces and worked as a duo. The best example of this is their cooperation in Thor: Ragnarok (2017). Loki then pretty much sacrificed his life when he tried to kill Thanos on Thor's behalf and he also gave up the Space Stone to save his brother.
Nebula: Joining The Good Side
Nebula was originally a major villain in the first Guardians of the Galaxy (2014). She reconciled with Gamora later on, joined the team, fought against their enemies, and helped to save multiple superheroes.
Most notably, Gamora helped Tony Stark after the snap happened and she also killed her past self to save everyone.
Ego: Being Peter's Biological Father
Ego isn't a good father. He was responsible for giving Meredith Quill the cancer that eventually killed her. And he also was willing to sacrifice Peter for his own benefit, just like he sacrificed many of his other children. However, there's no denying that without Ego's egoistical nature, there would be no Peter and the Guardians of the Galaxy would be a much different team. That is if they would form in the MCU in the first place.
Ultron: Creating Vision
Speaking of villains creating new characters, there's also the case of Ultron creating Vision. When Ultron did this, he had different plans for everyone's favorite synthezoid. However, as the fans know, it didn't work out. Vision joined the Avengers instead and fought by their side. He even formed a romantic relationship with Wanda Maximoff. Not a bad resume for a superhero who was just 3 years old when he died.
The Winter Soldier: Turning His Life Around
Winter Soldier is one of the most complex villains turned heroes in the MCU. From hero to a villain and again to a (tentative) hero, his journey has been long, difficult, and tragic.
Bucky has done many remarkable deeds, but one of the bravest ones was trying to start again and help the world after everything his enemies had brainwashed him to do - be it fighting Thanos's armies in Wakanda or fighting alongside Sam Wilson's Falcon.