The U.S. government cannot initiate any registry of any religion. We already have a registry of sorts in our immigration records and in the IRS list of tax deductible organizations. Why would the USCCB be involved in that and what could it possibly say within its competence?

I generally advise organizations and people to obey the law and, if they think it to be a bad law, to work to change it. Anyone has a right to contest an administrative order, and that includes Catholic colleges.