They are likely to be charged in Federal Court. The police officers will have the same rights and judicial process as anyone who is charged with a similar offense. It is anyone's guess if these officers will cooperate against others, seek some sort of a plea or sentence deal, or stand trial.
If they plead guilty or lose at trial and are sentenced to incarceration, there are prisons throughout the United States that house federal prisoners. I am sure steps would be taken to protect the officers from other inmates who may have issues with them.