Obviously not all churches have the same beliefs about the legitimacy of self-defense and defense of others as does the New Life Church. This brings use to the second violation of the First Amendment. The morality of using deadly force when necessary to protect innocent lives is a strongly debated topic among various denominations. The early Christians disagreed on the topic. Historically, the standard Jewish and Catholic view was that self-defense was a right and defense of others was often a duty. Some Christians, particularly since the 20th century, take an opposite view. Likewise, many adherents of the major religions of Asia also support self-defense, while some (especially some Therevada Buddhists) do not. These doctrinal differences about self-defense represent very important, sincerely-held differences in religious beliefs. A religion is, after all, not just about the forms of ritual; religion is especially concerned about providing guidance for moral conduct at moments when a person may face decisions involving the end of life.
The state, of course, must be neutral between the various religious beliefs. The state should not compel a Quaker to shoot someone who is trying to kill her, nor should the state forbid a Baptist from saving her own life. The CHL prohibition in churches violates the Free Exercise clause because it prevents self-defense by members of a religious community, when they are gathered as a community, even if key tenet of the religion is the communal duty of the adherents to protect their fellow adherents.
Moreover, the CHL ban also violates the Establishment clause because it favors some denominations over others. In effect, the statute privileges pacifist denominations over non-pacifist ones, by forcing the non-pacifist religions to obey pacifist standards of conduct in their own houses of worship. This is not only a Free Exercise violation, it is an Establishment clause violation, because it plainly creates the message that the pacifist way of being is the only way of being which the state will allow in any church, anywhere in the boundaries of the state.
This is from the Volokh Conspiracy. As with everything over there, the comments are worth reading too.
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