DNS is a service discovery protocol! And a rather robust one, too. Don’t forget that.
AWS doesn’t want to expose to the customer all the dirty details of how internal routing is done. They want to publish a single regional service endpoint, put a SLO on it, and handle all the complexity themselves. Saving unnecessary complexity from customers is, after all, one of the key value propositions of a managed service. It also allows the service provider the flexibility to change the underlying implementation without impacting customer clients.
I’m not sure the best response to “the reconciler had a bug, and other reconcilers might, too” is to replace it with an entirely new and untested service discovery protocol. A proposed compensating control to this bug might be as simple as “if the result would be to delete the zone or empty it of all RRs, halt and page the on-call.” Fail open, as it were.
Also, anyone proposing a new protocol in response to a problem—especially one that had nothing to do with the protocol itself—should probably be burdened with defining and implementing its replacement. ;)