Honestly, the main problem with splitting off origin civics is that (unless you can pick more than one), you're giving up some of the most fun combinations in the game. Fanatic Purifiers + Post Apocalyptic are a match made in heaven, both for gameplay and roleplay. Likewise with Life Seeded + Inward Perfection and the list would likely go on.

Pretty much the only way this would work is if you allowed everyone to pick 2, with a large number of minor options that allow for a decent boost. Things like starting with certain techs (Robots, for example), advantages in the starting system (maybe a small colony on a second world/habitat in your system would work, especially since tech penalties are going to be district-based soon anyway), or in starting leaders (a couple levels all around). But those are still kind of shoddy compared to all the game-changing options, since they are basically there as a way to NOT pick other origin civics, rather than because they are interesting on their own. Which is the real issue with the idea. Origin civics basically force every empire to have a unique or interesting backstory in a way the current civic system doesn't.