Normally, people are prosecuted in the court of whichever entity controls the land where the protest took place. Sometimes, jurisdictions overlap, and we can be prosecuted in more than one court. The various prosecutors get to decide where the case will be tried. Occasionally, one set of activists is prosecuted in state court and another set in federal court during the same campaign. If you have the qualifications for the job or school, a civil disobedience arrest is not likely to stand in your way.
Many institutions are actually interested in people who have consciences.
Many teachers, lawyers and health care professionals have engaged in misdemeanor-level civil disobedience. We are not aware of any who have actually lost their licenses, although some have been hassled by their respective bureaucracies. However, felony convictions, as opposed to misdemeanor convictions, could well result in temporary or permanent suspension of professional licenses. Just Cause Law Collective.