In addition, those that are most vocal are some of the most important users on Reddit. They make the community what it is. If you loose them, then rest will leave soon after.
Most of these are the largest subs because new users are subscribed to them by default. Default subs are just faceless crowds that don't have much of a community. You're defining "value" in terms of the aggregated number of eyeballs looking at ads, which I suppose is one measure, but the value of a site to a user is what it shows to them. They get this value from the subs that they choose to subscribe to.
For example, the sub that was directly affected was IAmA, a default sub which in its current celebrity-focused incarnation is no more a community than the audience of The Tonight Show is a community.
That they're also unhappy and have the same list of complaints strongly suggests that reddit isn't doing a good job supporting their communities.
/r/askscience is comparatively poor quality. Wrong answers are often given with no repercussion. Answerers are often entirely unqualified to answer question. This is arguably worse than no answer at all. I would not consider it a quality subreddit.
What you see on reddit is: people blowing gossip out of proportion on the subreddits who allow it. Those that "went dark" are probably the reasonable ones to avoid to avoid poor content.
Some peole are doing what they can to make this incident appear as being the same as the fatpeoplehate banning outrage, but this is different.
So yes, I 100% see the shit collecting where the shit already is. I had literally no idea there was drama until I came to HN.