Cooper says,
To be sure, the major objectives of the war – preserving the Union of the United States and abolishing slavery – were achieved. However, underlying the broad war objectives were assumptions [emphasis added] regarding the political transformation of Southern government and society; that transformation was unsuccessful.
As Union troops occupied Confederate territory there were still functioning governments in place, particularly at the county and municipal level (just that is worthy of a thread). But remember, government played little role in everyday life, particularly in rural areas. If slave state governments had a salient function it was to control the slave population. Lincoln's plan was to have ten percent of the antebellum voters constitute the next – not new – state governments and begin the process of bringing the states, not the people, back into sorts with the U.S. But Lincoln died. If the U.S. Army had a role post conquest it was to prevent the resurgence of Confederate military power.
Then come Cooper's assumptions, well, not his, but a new political agenda. This is both a continuation of the Civil War and even a new Civil War with new war aims completely apart from Lincoln's response to Fort Sumter. I think it's fair to say there were two occupations, one purely military, e.g., Sherman in Atlanta and Butler in New Orleans, and then the other a purely political program where troops are sheriffs, marshals, etc. I don't think the soldiers functioned as tax collectors, judges, county clerks, or operated state hospitals.
As for terrorism, intimidation, and ballot box stuffing, welcome to the United States of the 19th Century. Although other U.S. communities did not experience lynchings, there were gangs of toughs in Northern cities influencing voters and fraud at the ballot box. (In my study of Kentucky, an incumbent sheriff might have a saddle bag full of John Doe warrants and would arrest voters who voted against him (no boxes in those days, votes by voice). That was in the early 1800s.)
So, did the U.S. Army fail to do what the Radical Republicans wanted? I suppose so. An underfunded Army is a pretty poor instrument for social and political change. Did the ballpoint pen fail to paint the barn? Did the Army succeed in suppressing the shooting until all states were readmitted to the Union? Yes. Perhaps the Army's Mission Accomplished (apologies for modern politics) was in a hotel suite in New York in 1877 when Hayes was chosen president and the South got its harbors dredged. The South got their governments back, on their terms, of course and they were able to write their own history.
The Freedmen were left out of this, of course.
P.S. Co. B of the 7th U.S. Cavalry was on occupation duty until the beginning of 1876 when it was ordered to rejoin the regiment at Fort Abraham Lincoln for a campaign against the Sioux.