There are major flaws in the reasoning, just some:
"An oft-proposed alternate name for Kirtland’s warbler (named for Ohio naturalist Jared Kirtland) is jack pine warbler. Jack pine’s scientific name is Pinus banksiana. The specific epithet honors English naturalist Sir Joseph Banks. Dig deep enough into his history, and flaws will be found. "
The author mixes up English names (an alternative for Kirtland's warbler) with the scientific name for Jack Pine and argues that 'dig deep and flaws will be found'. The only flaw I see is mixing up things in his reasoning. I often see (in this very topic as well) that contra-change arguments try to mix the subject of discussion (ENGLISH names) with scientific names (names that aren't changed and aren't the subject of the discussion), and don't (or don't want to) understand the difference.
Another example:
"Many non-eponymous names are hardly descriptive. Who knows what mallard means?"
That's a false argument: You cannot argue that non-eponymous names are not an improvement, because some non-eponymous names are non-descriptive: ALL eponymous names are NON-descriptive. So ANY change towards descriptive names, is an improvement in description.
Another example:
"One huge asset that ornithology has that very few other disciplines in the natural sciences have is a stable system of English names."
Wrong. As I mentioned in this topic (or the other), English names are in constant flux. Just read here:
English Name Updates – IOC World Bird List . The last 2 updates saw 5 eponyms being erased: Cabanis, Major Mitchell, Hunstein, Cockerell, Worcester.
As a consequence, the author states:
"A large-scale change in English names will result in years of confusion, outdated field guides, and numerous other long-lasting hassles."
Current field guides get refreshed / new prints every couple of years. I am using my 3rd version of the Svensson guide, and I haven't even openened the last one (still using the first with all my notes). And this is without major name changes: new versions come out because better drawings / ID features / subspecies are depicted. I wonder if Americans still use their 20-year old field guides ignoring 10-20 splits in all those years?
one more:
"Legions of buildings, cities and towns, endowments and scholarships, streets, and much more are named honorifically. "
As mentioned (e.g. by me), comparing a building, city, ... (or any man-made object) to a living object when arguing how something could be named, is apples vs. oranges. We can do better with birds than we often do with streets. If the standard is this low (naming living objects, some having existed even before humans existed, after one single individual human being... I just find it weak to name something extraodinary in nature with a human-centric name. But that's me.
last:
"Resistance to the proposed AOS name changes has been widespread and opponents probably greatly outnumber proponents. To me and many others, the logic behind purging eponyms is largely baseless — at least its advocates have failed to make much of a case. The logic behind arguments for retaining existing names makes far more sense and maintains long-established stability."
It seems the nay-saying author resorts to the only argument I see over and over again: stability, status quo, being afraid of any change. Just turn things around: the logic behind keeping eponyms is largely baseless, and those who advocate the status quo have failed to make much of a case. IOC doesn't keep the status quo, even though they say they are neutral, eponyms are going out, but Americans want to keep it for whatever reason.