The official policy of the USA was that the former Confederates had engaged in a rebellion, and they were pardoned for the offense of treason. De facto, Davis and millions of other former Confederates accepted their pardon. They took advantage of the rights and privileges that the pardon offered them. Indeed, many former Confederates complained bitterly when, for example, their mistreatment of the freedmen resulted in temporary disfranchisement. They had no problem with the benefits the pardon provided... it was an offer they couldn't refuse. They certainly weren't going back to war to establish their rejection of the pardon..."A pardoned person must introduce the pardon into court proceedings, otherwise the pardon must be disregarded by the court. To do that, the pardoned person must accept the pardon. If a pardon is rejected, it cannot be forced upon its subject" Burdick vrs US
Until someone is actually charged with a crime, and the pardon introduced into court to avoid trial, there is no acceptance of the pardon and no implication of guilt. Someone pardoned can still choose to stand trial to prove their innocence.....its odd how often the most important part of Burdick vrs US is ignored. So Johnson proclamations carry no implication of guilt, as the pardons were never invoked to indicate acceptance, nor any need of anyone to even accept a pardon to avoid guilt.
Burdick does say acceptance of a pardon imply's guilt, but the actual focus and point of the ruling is there is no such acceptance of the pardon or guilt, until actually introduced in court against an actual charge\conviction...........
Find it odd that anyone would subscribe to 1 man could make the 6th amendment pointless.
The magnanimity showed to the rebels is somewhat unprecedented in world history, and many of them realized it. Of course many (most?) of them were bitter that their cause was lost, but they realized the pardon was a means to move forward after their defeat. It is worth noting that if Andrew Johnson had been impeached, the next president might not have been as magnanimous as Johnson, and things might not have gone so well for Davis. See the article "In 1868, the fate of Jefferson Davis's neck swung on Andrew Johnson's impeachment."
There is this notion that Davis was almost salivating at the idea of going to court to fight for the legal recognition of secession. But this may be apocryphal. At least two sources I've seen indicate that the Davis defense team was preparing to make the argument that the 14th Amendment already punished Davis by preventing him from holding public office in the future and that further prosecution and punishment would violate the Double Jeopardy Clause of the Fifth Amendment. This implied that he had committed treason, but had been punished enough. Whether repentant or not ~ and Davis was unrepentant ~ his actual defense strategy was more practical than ideological. But it was all rendered moot.