^And apparently Ambassador Fox had the power to send Scotty to a penal colony, with no mention of trial or court-martial.
Yeah, that was terrible when Scotty was gone to prison for all those years.
Not to mention Ambassador Sarek's contention the Tellarite ships were caught carrying dilithium mined on Coridan. The Rigel miners withholding dilithium from a starship that was spiraling down over some women. The plan to conquer Organia before the Klingons could.
I never got the vibe in TOS that the Federation or its citizens were all that benevolent.
Sending two men to negotiate with the ruling council is "conquering"?
The Tellerites were criminals, hence the "illegal" activity.
The miners were secluded and didn't feel beholden to Kirk showing up. Mudd complicated things, I think they may not have had a problem selling to Kirk if Mudd didn't start promising women.
So, based on about 400 people the billions of Federation citizens don't seem benevolent? I think your sample is too small for any judgements.
If you want something not benevolent, look at the institutionalized racism employed by the Stratos City Dwellers agains the Troglites. That, for me, hurts the Federation's image as a nice place to live more than anything you mentioned.