"IBM employees are taking a public stand following a personal pitch to Donald Trump from CEO Ginni Rometty and the company's initial refusal to rule out participating in the creation of a national Muslim registry. [..] Now, some of those who were horrified are going public, denouncing Rometty's letter and asserting "our right to refuse participation in any U.S. government contracts that violate constitutionally protected civil liberties.""

This literally isn't a right.  You can refuse to provide the service for which are employed, sure, but your employer can then refuse to provide you payment or continued gainful employment.

There exists no right to get paid for a job you refuse to do.