The way she describes it, it was a sensible choice. Various things are being promised that she, as Chief Engineer, does not think will happen. Given what happened with Ellen Pao it's not unreasonable for her to assume that responsibility for those failures could easily be put on her when the inevitable happens.
What's the point of being a Chief Engineer if you can't even get some software (the mod tools) written? That seems like an awfully low bar for someone in that position, and to throw in the towel after she barely started seems to speak more to her character than any problems with Reddit. I mean... you hire someone for a top technical position and they quit when the first bump comes along? That's ridiculous.
I have no idea what's going on inside reddit, just my two cents / devil's advocate thing.