Also cartel knows who are the key witnesses. It is not like the El Chappo discussed his business with infinite number of people. I would say 10-20 max if not less. So they just make a list and see who is present/not present and where are their families.
Though I am not even sure prosecution needs star witnesses. I don’t think there is a juror left who has no opinion on El Chappo.
The bigger problem is that dealing with El Chappo, killing or otherwise, is not actually solving the problem of cartels having nearly infinite resources to pursue informants/witnesses.
In a way dealing with cartel is like dealing with a state actor, but without traditional tools because they are outside the international law.
The only way is legalize the whole thing to bring drug trade into legal framework.
In the end the only leverage USA has is its market. So if they give market to legal entities, cartels and violence associated with them will go away.