Barriss isn't evil, she's confused and frustrated, she sees herself as a freedom fighter and that has taken her down the rabbit-hole of "terrorist" without realizing it. I can't imagine she WANTED to frame Ahsoka or any Jedi, she's trying to protect the Jedi and the people from bureaucracy and short-sighted decisions that have led to war and destruction on a galactic scale by the order she's watching tear itself down.
My real frustration goes to the mix of this and Force Unleashed totally undoing the previous stories. Barriss is younger (and evil, and not a healer), Dengar is much older, Greedo and Bossk are not only older but active long before previously stated, Sy Snootles is an assassin for Jabba when she should be too young to even be the luckless wannabe singer she is just before ROTJ, Anakin had a Padawan, Dathomir is well-known, Darth Maul is alive and has a brother, Jabba has a kid, Karen Traviss' books are completely wiped out of existence, etc, etc, etc. Even from a visual standpoint, all the Jedi get new duds for a short while, then go back to their old uniforms just prior to ROTS (when the war is still on). This isn't the reboot Star Trek or the post-Crisis DCU (or post-Flashpoint DCnU), where it's a new timeline and the previous stories still work in another alternate universe. This is just steamrolling over earlier stories whenever it seems like a good idea to someone at the time (and, really, is bringing freaking Darth Maul back ever a good idea?). Truth is, The Force Unleashed was worse about this than The Clone Wars is, but it's a game. Games have always been of dubious canonicity (did Jabba really hold a demolition derby with Boba Fett and Sebulba's son?). This is supposed to be highest-level canon.
Star Wars EU used to be cut-and-dry. This happened, and this happened, and that happened. There were "Infinities" outside the normal canon, but, otherwise, everything fit relatively painlessly. Sure, there were minor inconsistencies, like how the end of the original Clone Wars sorta didn't jive with Labyrinth of Evil, but it's one thing to figure out exactly where Mace is at a given time, and another to say that Mace was off-world at the beach with his lover, Kit Fisto.
It started unraveling around the time that someone decided the Marvel series was all canon, no matter how badly it fit, and brought back Lumiya. But it gets worse and worse. I pity anyone who tries to figure this s*** out now; it's worse than the Star Trek "EU" with all its contradictions. For me, it's not fun to try to decipher what happened and what didn't, particularly when the steamroller is as weakly-written as I find Clone Wars to be.