Why did the Federation tolerate some elements of Vulcan culture that actually may cause great harm to individuals?

[The Wormhole]

Before any civil war can't it be said the nation shares a common military?

But that doesn't seem to be the case with the Federation as depicted in Journey to Babel. To use your earlier comparison that the Federation of TOS is like the UN or EU, than those nations still maintain their own militaries with some nations having mutual defense pacts with others. There is no unified military responsible for defending the entire UN or EU. Indeed, many of the modern alliances like the UN, EU or NATO have their treaties worded very carefully to avoid a "you attack one of us, you fight all of us" scenario. Which I suspect was the intent of the TOS Federation.

 

[kkt]

The Federation and Klingons became allies, and I'm still waiting for someone to give the official Federation position on Klingons having slave races (according to TOS, ENT and Disco) while being "good guys"

They must have a very hands-off attitude. Perhaps too much so.

Allies is very different from being Federation members! You can be allies with a country that you have common strategic interests with even if you don't approve of everything they do.

As far as Vulcan, some marriages are arranged, but are they seem to be arranged with the consent of the people concerned.

 

[kkt]

I'd say the Federation definitely did not share a common military in TOS. After all, in Journey to Babel it's stated that there are Federation worlds on the verge of going to war with other Federation worlds. That'd be a bit tricky if they all shared a common military.

The intent in TOS was Starfleet was strictly an Earth organization.

I don't think that's the case. TOS had Spock in Starfleet, and USS Intrepid crewed entirely by Vulcans referenced. Clearly in Babel Federation members did have their own military organizations, but Starfleet was also shared between all the Federation members.

 

[Nerys Myk]

I'd say the Federation definitely did not share a common military in TOS. After all, in Journey to Babel it's stated that there are Federation worlds on the verge of going to war with other Federation worlds. That'd be a bit tricky if they all shared a common military.

The intent in TOS was Starfleet was strictly an Earth organization.

At the beginning yes. But most references to that were phased out by the end of Season One. OTOH, TNG tends to be "human this" and "human that". Which also makes one look askance at the "multi-cultural" Federation. The whole "go back to Earth" thing Q was pushing in EAF made no sense.

Q: Thou are notified that thy kind hath infiltrated the galaxy too far already. Thou art directed to return to thine own solar system immediately.

Then goes on a humans suck rant. Come on. The Enterprise probably has many species on it. They swinging by Qo'no'S and Betazed on the way back to Earth?

 

[The Wormhole]

I don't think that's the case. TOS had Spock in Starfleet, and USS Intrepid crewed entirely by Vulcans referenced. Clearly in Babel Federation members did have their own military organizations, but Starfleet was also shared between all the Federation members.

Starfleet was meant to be an Earth organization in TOS, that's stated multiple times in dialogue and indeed was meant to be the reason why with the exception of Spock, the entire crew was human. And in Spock's case, he is half-human.

This gets overlooked given that TAS and TMP later retconned other aliens serving in Starfleet which led to how Starfleet was depicted in the rest of the franchise as the service everyone in the Federation could serve in regardless of which world their from.

I grant you the Intrepid is an oddity in TOS, though there have been varying theories in tie-in material suggesting that Intrepid was just the English translation of the ship's Vulcan name, to it being an Earth ship that the Vulcans purchased. You'll note The Immunity Syndrome doesn't actually state that the Intrepid is Constitution class, that's just an assumption everyone has made based on it having a crew of 400.

I'm just going to ignore the fact that it was referred to as a Starship and that "Starship" automatically meant Constitution class in TOS.