Roddenberry's Trek was never a utopia.
Cyrano Jones, Harry Mudd, Captain Tracey, Kodos, criminal penitentiaries, and that's just TOS.
Even TNG wasn't as much of a utopia that people think, Tasha's traumatic background was from a failed Federation Colony for example. If Berman was following the "vision", he also introduced rogue admirals (Kennelly and Pressman), and the Maquis.
Well I think the idea was that Earth was a Utopia, but even that never fully held true.