That disproportionate response to what comes down to an organizational shortcoming on their end made people upset, I'm not sure what they expected.
They just don't want Canonical or Fedora to ship a theme that makes all applications that didn't come bundled look like shit. If you like the Windows 95 Hotdog Stand theme, you can configure that and everybody probably agrees that that's great. If you inflict that pain upon yourself, that's your problem.
The current "solution" to themes breaking applications is to just not follow the system theme any longer. Everything gets packaged with a hardcoded theme in a sandboxed environment and you'll just have to live with that.
Now you know why the application developers are so loud and angry. We can’t have nice things because distributions shipped broken default configurations, and that’s messed up.
If you have a feature that is used by one customer out of thousands but it's causing problems at every update you push out. It might be better to remove the feature and fire the customer, than to keep supporting it no matter what.