Lol, whatever. First they are a business, they are not regulatory body or a law enforcement agency, like all businesses they have every right to refuse service in order to protect themselves and the market. The self clearing broker dealers are now on the hook and well they do not like having unregistered certs sitting in their accounts that they are likely going to have to eat. So they are also protecting themselves from being stuck with crap as they are legally allowed to.
Protecting "the market" by screwing up ALL shareholders with huge fees? In which world of fantasy do you live in? By the same reasoning, your water company could cut your home's water supply and go on buckets at $50 each just because they think there is a dead rat in the river.
Tracking frauds is the SEC's job not theirs. If they find something suspicious they can always report it to the SEC for further investigation.