Kind of. Reddit cares a lot more about keeping the defaults around than keeping the smaller questionable subreddits around. I genuinely don't think they want to ban the distasteful but non-harassing subreddits (partly because they don't want to be known as a site that would ban those subreddits), but if one of those subreddits decided to one day get up and leave of their own accord, they wouldn't shed a tear. If, say, /r/IAmA decided to get up and leave, that would be a problem. This happened once [1], it was a problem, and (IIRC) Reddit management stepped in.
So yes, they're disconnects. But one is a disconnect between a userbase / the moderators of subreddits that Reddit the company is not very invested in keeping, except to the extent that in general, they want to keep subreddits that don't break rules. The other is a disconnect between subreddits that Reddit relies on.
That's why when tension 1 flared up a few weeks ago, Reddit banned some subreddits and implicitly threatened others with banning, and when tension 2 flared up yesterday, some other subreddits threatened to shut down and successfully forced Reddit to care.
They don't sound unrelated: both complaints seem to point towards a fundamental disconnect between reddit's management and its userbase.