Lin En proposed the Penitent Crusade not because he was afraid of the Council or the Inquisition, but because the Lamenters had truly committed treason, even though they had been deceived.
The Lamenters were truly innocent, but they had also genuinely done wrong. The Penitent Crusade was a just sentence.
Yellow Pelt sent the Adeptus Custodes to protect only Lin En. He handed the Lamenters over to Lin En because Lin En wanted them; otherwise, Yellow Pelt absolutely would not have given them to him. Neither Yellow Pelt nor Lin En wanted to shield them. They truly deserved to go on a Penitent Crusade. By accepting the Lamenters, Lin En also had to accept their crimes. Yellow Pelt and Lin En would not interfere with the Imperium's judgment of the Lamenters' crimes unless it truly went too far.
The Emperor's orders were indeed supreme, but the Emperor also upheld fairness and justice. The Emperor would not shield crimes. Covering up crimes was an extremely bad thing to do, especially when the crime was treason.
The High Lords Council had done nothing wrong in handling the Lamenters' case. They had merely been led astray by the corrupted Inquisitor-General, resulting in an excessively harsh judgment.
The Grey Knights had done nothing wrong in coming to deal with the Lamenters. They were enforcing the law properly. They had not attacked only because the Adeptus Custodes were too powerful to defeat.
The Adeptus Custodes had not attacked the Grey Knights because, in truth, they were in the wrong. They acted so imperiously because they were accustomed to throwing their weight around. Their reason for attacking the Grey Knights was that the Grey Knights had offended the Emperor's dignity, but in essence, they were obstructing law enforcement.
Lin En stopped the Grey Knights because the