BELIEVABILITY has worn itself out on Trek because of aliens. They are treated too commonplace and accepted too readily as well as believed of every word that they say. I believe Spock was only aboard because they were going where no man had gone before and Starfleet needed an alien's perspective. What if they found out the Vulcans were some super advanced higher meta-life form come to test us? They could have been Talosians. That would throw a wrench in the Federation's abilty to understand the truth about the universe and aliens as well as Mr. Spock who might have been part of the investigation. He might have known things about aliens that he wasn't revealing. As Q said, the jury might still be out on that, though any future developments aside, Spock to me was still Questor - an alien without a home, per say, but still an alien. Understanding aliens is the focus of Trek but it need not contain so many humanoids. Spock should have been a rarity on a Starship and only a few races should have been seen or heard like the Vulcan/Romulans, Andorians, Klingons.
Spock could have obviscating the truth about his true nature and that of the aliens. That would and should be intolerable to the Federation. TOS to me was a one offer - an extended rescue mission that turned into a fantastic odessy all pretenses of it's five year mission aside. The fact that Spock prooved to be trustworthy doesn't mean or change anything. He's still an alien, if only half and it was probably because he was half that they put him in there. They may not have put a full Vulcan in. Too risky in every way that's meaningful.