Nixon: "Yeoman Radford had all of this information and if he had been prosecuted, it was my opinion that there was a very great risk, because of his obvious emotional instability, that he would blow the whole thing. … The war in Vietnam would have continued for a while longer. … I had to make a decision."

Gee, we wouldn't want the war to continue for a while longer, would we, Dick? https://www.lbjlibrary.org/media-kit/chennault-affair

The only beef Nixon had with the "deep state" was with the parts that he didn't control himself.