Clone Wars era Siobhan is...hard to pin down and define. A good deal of her backstory would have to be changed because frankly I can't imagine the Jedi Order tolerating her in their ranks. After all, she is openly darkside now and even when she was a Jedi did not care about their rules and beliefs. Just hated Sith. And her teacher, Adril, was a terrible Jedi as well!
So I guess Sio winds up as a rogue, darkside-leaning forcer. Probably a mercenary of some sort. If she hires with the Separatists, she ends up dead by being gunned down by lots of clones, Jedi or Vader. One intriguing possibility would be Siobhan ending up on the Imperial side and helping carry out Order 66. Inquisitor Kerrigan seems like a good possibility...especially if a certain [member="Mirien Valdier"] is around as well. I'm quite certain that Sio would wind up getting purged and killed at some point though (though tin pot dictator Sio being a warlord on some banana republic, rim planet after the Empire disintegrates has its charm).
Alternatively she ends up as a hardcore, darker and edgier Rebel, which was actually the path she would have taken on TGC if I'd continued with her there since she voluntarily left the Jedi. And [member="Tegaea Alcori"] coincidentally was a Rebel back then and they were friends. Only Siobhan, if she falls as far as her current incarnation has, would be far closer to the terrorist than the 'freedom fighter' type...so it's possible she comes to a bad end there as well. Unless there's a....restraining influence.