It seems to me that there are two major, unrelated tensions in Reddit at the moment:
1. Certain people want Reddit to be a haven for free speech, including speech that coordinates abusive actions. The Reddit admins (current and past) don't think that's what Reddit should be.
2. The Reddit admins have a poorly structured relationship with the volunteer mods of their largest subreddits. IAmA's full-time paid staff member was the biggest evidence of this poor structure, but it has never worked well. [Even if AskScience's mods are professional scientists, they're still volunteer AskScience mods.]
The first tension is between the Reddit admins and a few non-default, somewhat small subreddits (some of which have been banned in the last few years); the second is between the Reddit admins and the large, mostly default subreddits. In both cases, people are fed up with the admins, and in both cases, this may have been going on for years, but they are fundamentally unrelated complaints. You can believe that the admins are doing fine on one while believing they're doing an awful job on the other.
By and large, the people who complain about Ellen Pao's leadership are complaining about tension 1. Tension 2 is organizational debt that Ellen Pao clearly inherited, and while the buck now stops with her to fix it, nobody thinks it's a problem of her making. People unhappy about tension 1 (including, potentially, mods of smaller non-default questionable subreddits) may use today's tension-2 event to vent anger at the admins, but that doesn't mean there's only a single complaint about the admins.
I'd also argue that if tension 1 were really a problem (i.e., Reddit staff were wrong), Reddit would be obviously going downhill, while tension 2 can fester as organizational debt for years before exploding, if everyone is well-intentioned.
(My personal view, if it didn't come through, is that the admins are in the right on tension 1 and if anything aren't aggressive enough, but have been doing a bad job of resolving tension 2 for years.)