2nd Ending
The second ending where Mrs. Peacock did all the murders is just as bad for Col. Mustard as it is for Mrs. Peacock. In this ending Wadsworth states that he works for the FBI. Mustard had already admitted to an FBI agent that he was selling Air Force Radios on the black market. Not only would he be given a dishonorable discharge, but would stand trial for treason, and could face the death penalty.
The others wouldn't have as much of a problem.
While Ms. White may have admitted that Yvette had an affair with her husband, she never admitted to killing him.
Prof. Plum admitted to having an affair with a patient and losing his license, but ultimately the FBI wouldn't care enough about that to report it to the UN.
Likewise with Mr. Green. Being homosexual wasn't a crime, so he wouldn't be arrested and there would be no need to tell the State Department.
Miss Scarlett admitted to running a brothel, and bribing a cop, but like Mr. Green said, half of Washington would be implicated if she were exposed. So even if they tried to charge her, there would be plenty of powerful figures pressuring the DA to drop the charges.