Good post. You basically admit in the end that TOS is an utopia despite having denied it earlier and I agree. I think if utopia is a better world without cynicism and with the desire to become even better we can apply the term onto Trek.
When Kodos is killing half the population on Tarsus IV it is not normal and it doesn't make people despair but actually inspires one young kid to become a Starfleet captain and fight against this stuff from occurring. Doesn't mean it won't happen again but it doesn't mean that it ever becomes normal in this fictional world either.
And this old trick from "The Devil In the Dark" which you mentioned, showing people messing seriously up but changing before it is too late, and which is also used in TUC and FC is IMO paradigmatic of Trek's approach to utopia. It is in the literal sense a non-existing place, something which you never reach but constantly strive for even and especially when you messed up.