(No, she's not, but that doesn't mean she's not worried about him. Riagan does have some points, but his anger blinds him. That's what's she's worried about. She's also feels bad since she can see he was honestly trying to help, but went too far, not to mention the tragedy the Fae caused the Dwarves.
Sakura beyond all else wants her friends to not fight, she knows the Prof is scared of him and she knows Pema likes him even less now. However they still have to work together, and she doesn't want them to fall apart. She doesn't just care about Pema and the Prof very much, she cares about Riagan too, so she's conflicted.
Not to mention she's seen how Riagan acted in the Watch Tower. She seen him treat the Prof with concern and even worry in the Watch Tower when the Prof was going nuts from hallucinations she's wondering if that was still evident in him or not. Even before that she's seen how he wanted to handle the Watch Tower alone and not let his guests come to harm. She sees that he cares about people, but he cares too much and gets too angry if they come to harm.
As Calien said it seems odd that he's acting this way even though the Prof risked his life, and sanity, to try to help Riagan. Even though the Prof couldn't do much, his actions were still there.
Sakura doesn't see in Black and White like someone like Pema, though the bad guys are still mostly black to her, she sees the grey as well, like when she learned more about the Order from the Professor their grey lighten slightly, very slightly but it is lighter. Riagan is a lighter shade of grey, he believes in Justice but at the same time his Justice is very near sighted, while the Order is still a very dark grey to her, though they might get a darker grey as the story gets on.
So it's not that she's taken Riagan's side, ie the abuse of the Prof was justifided, she's worried about Riagan because despite all this she still thinks of Riagan as a friend, a misguided friend but a friend. So yeah that's it.
I really should retcon the post before that but it could be that she doesn't know Fxeni is going to see Riagan.)