He hasn't said anything specifically regarding why he left the show. It might be because he wanted to focus on the comics. As he's the writer for the upcoming Rebels comic, The Last Padawan.
As for all these Disney conspiracies, so far they just appear to be a bunch of hogwash. Weisman is still working with Lucasfilm, just not on the show specifically.
Here are some choice quotes from an interview he did with Newsarama:
Greg Weisman: When I came aboard Star Wars Rebels, Simon Kinberg and Dave Filoni had already created all the lead characters. I like to think I contributed, but the characters existed. One of the first things I did when I sat down with them was say, “let’s talk about who these guys were. How did we get them here?”
We did that for all of them, all six. We came up with really great stuff, all three of us and the Lucasfilm Story Group, came up with really great stuff for all their backstories. So for me, this is great! That was great material, and on an ongoing series like Rebels, you rarely have the chance to look back and tell those stories. As Dave is fond of saying, “Star Wars doesn’t do flashbacks.” Well, they do entire movies that are flashbacks (laughs), but they tend not to stylistically flashback in the middle of a piece.
So [the novel, comic and show are] all part of the same continuum that the Lucasfilm Story Group has been building for Kanan, and for all these characters, and part of the original work that Simon, Dave and I did when we first sat down and started breaking the show.
Weisman: (laughs) Yeah, I know! And if that wasn’t enough pressure, at the same time, you also know that there are legions of great fans who take this tremendously seriously, are religious about it. Fans that dress up as Stormtroopers, and more power to them, we want them to enjoy this as well! So that’s the tremendous challenge that we faced in making this show, is that this has to work on both ends of the spectrum.
The good news is, I think it does. The response to Spark of Rebellion has indicated that. That it has largely succeeded. And that’s thrilling. The fact that the ratings were good doesn’t hurt either! (laughs) It’s great to be creatively praised, but the fact that it did well commercially is nice too!
I’d go back to Young Justice in a heartbeat, and I’m thrilled to still be involved with Star Wars Rebels, doing this Kanan series.
Sounds like Lucasfilm and its Story Group are the ones calling the shots to me.
As for how the show has been going so far. It seems plain to me that these first episodes are all about introducing you to the characters, who they are and what drives them:
- Spark of Rebellion introduced Ezra and we got to meet the rest of the crew through his eyes.
- Droids in Distress setup a connection between our motley crew and one of the more famous founders of the Rebel Alliance. Expect this to pay off way later.
- Fighter Flight was about the dynamic between Ezra, Zeb and Chopper.
- Rise of the Old Masters touched on Kanan and his insecurities about his ability to train others. As well as introducing the Inquisitor.
- Breaking Ranks introduced another future series regular and revealed some of what the Inquisitor has been up to.
- Out of Darkness reveals some of Sabine's past and her reservations about what they're doing.
This first season is all about setup. Setting up who the characters are and where they're going. By season two with introductions out of the way they can plow straight forward and focus on paying off everything that they setup before.