There are laws limiting freedom of speech that were made in order to protect people. Such laws deal with things like hate speech where there is extreme racism or xenophobia, or in cases if someone wanted to give away classified information that could endanger people, or if someone called for violence or anything similar. Those things are all forbidden by law.
It is important to balance the two because if a majority has too much power over the minority then we have a situation in which there is a tyranny of the majority which means that minorities have no power and can be exploited or harassed. If a minority has too much power at the expense of the majority, then the country is not a democracy.
It is warranted. Civil disobedience was common during the civil rights era in the 60s where civil disobedience led to many victories in regards to the rights of the harassed African-Americans. However, they all went to jail because of their civil disobedience so it shows that they took responsibility for their actions, which in turn inspired people to support them.
The correct balance can be achieved through legislature such as the first amendment. A state has to be secular because it is a state of all the citizens, not just smaller groups. In a secular state, all religious beliefs are valid and protected and people can believe what they want without suffering repercussions. Beliefs and church going are private things that are not related to state governing so they need to be separate in order to protect everyone.
