I think there's a difference between Starfleet black ops and Section 31 operations. Yeah Starfleet can do shadowy things sometimes but at an accepted level of accountability. Section 31 comes in when you need anonymity or a scapegoat and sometimes it can be a scalpel like during the Dominion War and other times you need a chainsaw like in the Section 31 film, general peacetime so not as much need for finesse and if you need to blend in to the lawless underworld you need loud idiots who by standing out don't stand out. As for why Garrett was attached as a Starfleet liaison I think we're seeing the transitional period for the organisation, probably not known to just any old citizen or even officer but the upcoming Tzenkethi and Cardassian wars are likely to have pushed Starfleet's extreme measures and general screw the rules division much further into the shadows.
But overall yes, I think Section 31 is necessary, no utopia can ever truly exist, it will always have a seedy underbelly keeping everything in order.
But overall yes, I think Section 31 is necessary, no utopia can ever truly exist, it will always have a seedy underbelly keeping everything in order.