No. There "are" waivers for zoning irregularities. This is just a case of an over-reaching bureaucracy at work.
I’d get some endangered birds to nest in the treehouse, take pictures, and contact the EPA to say it can’t get removed for that reason.
Geez don’t you think they would have tried that first? The zoning doesn’t restrict building it prohibits it altogether and for the town to grant a waiver would mean anyone could then build a tree house or 2 or 3 of them.
How about someone buys your neighbors home, gets a zoning variance and after knocking down the house puts up a body shop?