The passage of time sees even long-time members evolving into an ethical grey area. Civil War showed that even the founders can shift their position. Like that conflict, the heroes acknowledge most of their mistakes to the public, but there are some things that the Avengers hold close, known only to the membership, and of course, long-time readers.
This article discusses spousal abuse and sexual assault
The Illuminati were a secret cabal of powerful heroes introduced in New Avengers #7 by Brian Michael Bendis and Steve McNiven. Iron Man formed the group of Marvel's well-intentioned leaders following the Kree-Skrull War, and they steered the direction of the Marvel Universe from behind the scenes.
The Illuminati hid the Infinity Gems to keep anyone from using them, sent the Hulk into space to prevent his rampages, and sought to deter the Skrulls from invading Earth. They even tried to protect Earth-616 from the incursions of parallel Earths. They failed in all these. It might be for the best that the Illuminati haven't reappeared since Secret Wars.