As with all of these discussions, the point of having Either be Foldable is not that you're going to call foldMap on an Either value directly. Instead, it is that you be able to pass whatever sort of foldable thing you choose (which Either certainly is) to a function that only requires foldability of its input. By removing or damaging the Foldable instance for Either, you don't simply prevent people from encountering problems that will be resolved the first time they test their software - you make a whole universe of nicely polymorphic functions unavailable for them to use without additional effort.
In particular, the idea that one should make all such functions partial by throwing an error is repugnant.