I am not surprised that some government (or, for that matter, private sector -- but especially government) employees think they have "rights" to jobs (or, rather, continuing paychecks for jobs) that they refuse to do.
I am surprised that there are lawyers lining up to file suits claiming such rights.
This is not that complicated, people:
If your religious beliefs (or any other principles you hold) require you to refrain from doing X, do not apply for or accept a job that requires you to do X. If you're already in such a job when its conditions or your belief change, quit that job and go do something else.
If your religious beliefs forbid you to issue marriage licenses to same-sex couples, don't run for county clerk or apply for a job at the county clerk's office (or, in this case, do hand in your resignation when the job requirements change in ways that conflict with your religious beliefs).
If you oppose the death penalty, don't throw your name in the hat for that position as executioner at your state's penitentiary.
If you keep kashrut or halal, don't call up the HR department at HoneyBaked Ham to see if any taster positions are open.
If you're Amish, a career at Uber may not be for you.
"Freedom of religion" does not imply a guaranteed paycheck, from the taxpayers or anyone else.