Mankind generally learns about the existence of mutants and aliens in most past TMNT incarnations, so I wouldn't be surprised if it happens here.
I mean there's now a LOT of mutants in IDW, there's no way all of NYC can go without talking animal sightings. It's inevitable at this point and this is where the human anti-mutant crusade usually starts in the series. And Bishop can rally his support among the people and fuel their hate ala Trump.