On February 2016 I sent Stardock a ticket about being able to set that a faction isn't part of United Planets. Stardock staff can look at ticket: #OKN-974-70473
Had mentioned this to Derek Paxton even earlier on May 2015. Seems that is how seriously Stardock takes the modding community.
So how to find a workaround for this? Factions that defy a single resolution leave United Planets forever and suffer a diplomatic penalty. In GalCiv 2 the penalty was even more severe as you couldn't create trade routes after leaving.
AI may defy UP based on accumulated dislike on certain resolutions. Once that limit is reached, the next disliked resolution will cause the AI to defy UP. The vote on the resolution is canceled and only a single faction can defy the UP per vote on a resolution. From what I've seen, the accumulated dislike is reset when a faction defies a UP resolution.
The dislikes can be accumulated through conditions based on Ideology(Benevolent/Neutral/Merciless?), a single Personality Trait and something called Status. Don't know about Status, but neither of the other two are helpful in having a specific faction defy UP. Personality traits are hardcoded, custom ones cannot be created. Custom Ideology trees can be created, but I don't know if they would make an impact in the AI's decision. Also in order to change these modifiers, the whole UPResolutionDefs.xml has to be overridden.