So, if you're in a government position that asks you to perform against your religious convictions/creed, your options are to act against your conscience or find another job? Freedom of religion does not end when we step outside a church as many would like us to believe. Liberty is not license; it is the freedom to agree or disagree. There needs to be accommodation and respect for the religious convictions of individuals both in and out of government. It is presently lacking.
If you take a job, with certain known job requirements, and you later decide that you cannot in good conscience perform the job so as to meet those requirements -- for whatever reason -- you have three choices:
Congress shall make no law respecting an establishment of religion, or prohibiting the free exercise thereof;It does not guarantee you the freedom to exercise your religion at your job to the point where you are unable to perform your job requirements (you are still free to exercise it elsewhere). You are welcome to fight The System if you wish, but the 1A "Freedom of Religion" does not guarantee that you'll win that fight.
That is, if your religion requires you, say, to wear a pendant with a Cross on it, that probably doesn't get in the way of doing your job. But if your religion requires you to be naked and carry a boombox with loud rap music blaring, that's likely to affect your ability to do your job effectively.
So to your point, does freedom of religion end when you step outside a church? OF course not. But it is inapplicable when you take a job with requirements and then refuse to meet those requirements.