I am not a lawyer, but I have a long standing professional interest in the ADA. It ain't over until it has been to court. The hurdle for the new agency rule is to demonstrate that this is not a violation of civil rights under the American's with Disabilities Act. For the past thirty years (almost) that's tended to be a high bar. How high? Well emotional support animals were flying because the airline industry didn't…
The FAA is acting under the assumption that this act gives them the ability to regulate differently than the ADA. However many of the changes made in this ruling are actually making the regulations more aligned with DOJ's ADA regulations.
So if a court were to rule that the FAA needs to follow the ADA rules completely the main change would be eliminating the new optional (airlines choice) form requirement for service animals.
Emotional support animals have zero protection under the ADA. They are only recognized under the Fair Housing Act (and is mostly an artifact of caselaw there) and under the FAA regulations being revised here.
Unless/until courts rule that emotional support animals must be allowed as reasonable accomidations in public places under the ADA (rather than just under the Fair Housing Act) I expect this exclusion of ESAs will be allowed to stand.