"The Pentagon has released a statement confirming that soldiers could be prosecuted for promoting their faith:"
That headline is absolutely nowhere near what is actually said. People in the military agree when they join not to spout their own religious beliefs because their statements may be taken as an official position of the branch they serve. This is something you agree to when you join, and by breaking it you can be subject to punishment. Just the same as if you went out and said we should use the military to kill off minorities or something. That's something many people might not agree with, but saying it in uniform would imply that it is a condoned position. Which it is not.
Chaplains are ALREADY not allowed to go out and try to convert people. Chaplains are there for people to GO to, not to go promote their own beliefs to others. So that section is stupid.