The fact that she "stood up" against some of the worst of Reddit shows that she was not the best suited for the job. Now before I continue, let me clarify that those banned subreddits were awful, as awful as all the threats and insults she received.
However, I wonder what was she thinking when she banned those subreddits, specially FPH. They were a bunch of trolls: did she think they were going to just shut up and stop harassing people? Nope, they weren't going to. Moreover, as the ban reasons were not completely clear (they were a bad behavioured sub, but the admins didn't show a clear proof of harassment with support of the mods) some redditors decided to support them, because hating corporate is always cool. A wonderful mix of a big community, with a high percentage of trolls, plus the "free speech" flag, plus the "corporate is destroying Reddit". The result is the chaos that happened in the days after the ban and the obvious damage to her reputation.
That was not the better solution to the FPH problem. There were other possibilities. For example, removing them from the front page to cut their growth in the early stages. Or, in the moment the imgur thing happened, issue a clear warning to the mods and tell them that the next offense meant a ban (they could've avoided further harassment or maybe could have banned them without such community backslash, giving the rest of the users a "see? they're bad, we told you, we had no other option" explanation).
But even with a bad decision on the FPH ban, she could have survived if it weren't for the /u/chooter thing. A CEO in a delicate position, with part of the community with doubts about her and another part directly hating her... firing an appreciated admin wasn't the best idea at all. I wouldn't have thought it would have created such a big outcry, but it was clear it was going to revive the Ellen Pao hating circlejerk. It was a suicidal move.
And, as you say, the bad part of these suicidal moves is not only the hate and the threats she received and the fact that she had to resign, but also the fact that is going to be taken as a victory for the childish trolls of Reddit. Basically, Pao screwed up really bad, and I think she made things worse in the harassment/hate field.