The federal government CANNOT allow its agents to be killed without drastic consequences to the killer, regardless of how justified the circumstances. The federal government CANNOT allow its agents (like Lon Horiuchi) to be prosecuted for "following orders".
To do otherwise would be to risk agents refusing to follow orders if they had doubts of their legality, or to refuse to undertake an operation if they felt the personal risk was too high.
The downside of hiring thugs as your enforcers is that a large percentage of them, while willing to commit atrocities to further their careers, are cowards when it comes to facing personal risk
Actually the Feds cannot prevent that. They lost their case where they contended Horuchi could not be tried for murder, but the new district atty in Idaho declined to prosecute.