... It’s a hard problem and I can see the upsides of Apple automating the clearing of truly abandoned apps from the App Store, but it seems like there ought to be a way for developers of not-updated-for-a-while apps and games to just log into Apple’s developer portal and hit a button to vouch that they still work and don’t need an update. ...

My guess is that this will become a huge topic in the next weeks because from a developer perspective it doesn't make sense to touch a perfectly fine running piece of software. On the other hand I can also understand why Apple is trying to "clean" the app store. The above quoted suggested compromise could be a good way to handle, in any case a better approach than the one Apple is currently pursuing.