Some light shed (paraphrased):
OSI does not release the names of the informants to anyone. It is like asking the president if he knows the names of the top FBI/CIA informants. It's not need to know.
All informants are documented. There are no "secret" informants, It doesn't do much good to have very many people know, how else to find flaws in leadership if the commander is the problem.
The informants featured in this article are referred to "dirty", because they committed a crime prior to being sought after for this purpose in return for leniency. I'm sure that there are informants that are clean,. Usually it deals with drugs, as finding the dealer is difficult. Additionally, all informants in the OSI are required to sign documentation stating that their seeking of information should not violate the law in any sort, which is contrary to civilan police informants which may break the law to assist in convictions.
That leniency does not mean their initial crime goes unpunished. For these cadets, it is separation without an Article 15 or official case. Additionally the Cadet (Thomas) I believe was relieved of his 180,000 fine for being separated in his senior year.
The freedom of information act does not apply to informants.
The OSI will neither accept or deny an informants identity due to security and safety protocols.
In short, these cadets were separated from the academy because of their initial violations. Being an informant does not grant a "get out of jail free" card.
Whether or not this violates the honor system, I'm not sure. It is a sucessful program apparently.
If you read the article again knowing all of that, the perspective changes quite a bit. None of the cadets opposing are saying "I was a perfect student, never did anything wrong or illegal, and they forced me to break a law and I got expelled."