Freedom of worship was the right to worship one's religion as one saw fit, provided that it did not involve committing a criminal act.
In 2376, B'Elanna Torres wished to revisit the Barge of the Dead by having a near-death experience induced. When Captain Kathryn Janeway refused to allow her to do so, Torres asked if the captain was saying she couldn't follow her religious beliefs. Janeway didn't want it to become a debate about freedom of worship, but Torres told her that it already was. Janeway then explained that there were limits to the things she allowed USS Voyager members do in the name of religion, giving the example of child sacrifice to a god as unacceptable. Torres called the comparison absurd, but Janeway said she was the one being absurd. After Torres explained that she didn't want her dead mother to be ashamed of her, Janeway finally acquiesced to her request. (VOY: "Barge of the Dead")