Yes-ish. The characters were villains, but the organization wasn’t necessarily. For instance, in Discovery season 2, Leland and his crew were the villains, but Section 31 was portrayed less as an extremist cabal and more as a misguided morally-grey organization. Less a blight upon the Federation and more an uncomfortable, but integral, part of it.
@setsneedtofeed captures it well. Instead of being a cabal of extremists doing illegal and immoral things because they think they’re connected to a higher purpose, they’re a semi-official CIA-like organization.
I guess what I’m trying to say is that Section 31 isn’t supposed to be a cool or semi-legitimate organization (with ships, insignia, etc.) but rather shadowy and absolutely beyond the pale of legitimacy where very few can stomach what they do. From an artistic/thematic POV, Section 31 should be there to show us that a good society requires work to maintain and that its undoing can come from within by those claiming to protect it by eschewing that society’s values. In other words, the ends don’t justify the means.