Perhaps you do not understand why Chaplain's do what they do, or something seems objectionable about their actions. Check here to verify what rights a Chaplain has.
1. The Chaplain has a right to exist in the Army. (US Constitution 1st Amendment; Katcoff v. Marsh) Rather fundamental, and therefore a good place to start. You don't have to like your Chaplain, but our existence is not only a protected right, if we didn't exist it would infringe on the anti-establishment clause. The government cannot force Soldiers into prolonged scenarios (e.g. war) where they are deprived of all access to the exercise of their religious practices.
2. Invocations, Benedictions, and other Ceremonial Prayers at mandatory events are authorized. (US Constitution 1st Amendment; United States v. Marsh and subsequent case law). When performing this prayer, it may be given without censorship or interference, including appeals to a specific deity (ie. praying publicly in the name of Jesus is protected speech, and not coercive). ().
3. The Chaplain has a right to refuse performance of religious rites and practices.
4. Privileged Communication supersedes orders. Reference the Manual for Courts Martial among other sources. In short, the privilege belongs to the one divulging information to a chaplain or their assistant under religious pretext conveyed by private means (not reasonably public information). No matter the content of the information, the information may not be shared when it is privileged, including in a court of law, or by court order. The chaplain must presume this privilege on behalf of SMs until it clearly determined otherwise.