It seems to me that Neely, in his usual slothfulness, only looked at the documents about Merrick in the Official Records series. If that is the case it is very possible that he did not even know about Merrick's house arrest, which is detailed in a letter by Merrick himself that appears in the court records for the DC Circuit but not the Official Records series. If that is the case then his neglectful treatment of the incident is more out of incompetence than anything else.
Neely, despite his fame in the world of court historians, is a very sloppy researcher. He's a major proponent of the claim that Ben Butler didn't meet with Lincoln to discuss colonization in 1865 - a claim he makes in his book the Lincoln Encyclopedia. His "evidence" of this is that Butler's Book suggests the meeting was held right before Lincoln left for City Point at which time Butler was not in Washington. Therefore, concludes Neely, they never met and accordingly never talked about colonization.
That is, of course, false as newspaper reports demonstrate Butler was in town the day that Lincoln returned from City Point and the surviving Hay memorandum in the Library of Congress proves conclusively that Butler and Lincoln met at least once during those crucial days - the morning of April 11th. All of this seems to have completely escaped Neely's attention. Nor does it seem to have occurred to him that Butler, who ADMITTEDLY states in the colonization passage that the juxtaposition of events is based on incomplete recollections, simply mistook the date of his known meeting upon Lincoln's return from City Point with Lincoln's departure to City Point.
In another curious case, Seward, on the strength of allegations in an unsigned letter written to General Winfield Scott, placed under military surveillance Assistant Judge William M. Merrick of the United States Circuit Court in the District of Columbia. Seward's terse order to Provost Marshal Andrew Porter directed him "to establish a strict military guard over the residence of William M. Merrick." Porter apparently interpreted this to mean something more than surveillance and asked Seward, "Is it desired by the honorable Secretary that the judge should be confined to his house?" Seward replied that such confinement was not expected and that "it may be sufficient to make him understand that... when the public enemy is as it were at the gates of the capital the public safety is deemed to require that his correspondence and proceedings should be observed." The same day that he wrote Porter, October 21, 1861, the secretary of state also sent the first comptroller of the treasury this astonishing letter: "I am instructed by the President to direct that until further orders no more moneys be paid from the Treasury... on account of the salary of William M. Merrick." Merrick was never arrested, but Seward's order violated the Constitution's stipulation that judges' compensation "shall not be diminished during their continuance in office." [70][70] O.R. II, 2, pp. 1021-23. I am indebted to Howard Westwood for the constitutional point here.