Mary Surratt is indeed given a civilian trial after her lawyer is able to get a writ from a judge?
Just saw the Conspirator tonight too... ha.
I don't think it would have made much difference, honestly. They were out to kill the conspirators and put the final nail in Lincoln's coffin. The goal was progression under Johnson.
However, if the civil trial goes well enough for her and gets enough positive press in the South the government would see the potential for some serious spin. So in answer to your question:
A. It depends on the outcome of the civilian trial to some degree.
B. If the North can be rallied around the concept of the ACW being fought not for borders, but for the defense of the U.S. Constitution and it looks as though she is innocent or at least enough for public opinion to support her claims of innocence, and if the South rallies around Mrs. Surratt herself with enough volume... I could see her possibly getting a Presidential pardon.
Johnson ends the Lincoln fiasco while all at once promoting himself as the "hero" or the "good guy" of Reconstruction, neither of which he was in any way. He would see a grand opportunity to improve public opinion and increase public support of his (and later Grant's) disastrous modification of Lincoln's Reconstruction plan.
Whether she is pardoned or goes free, she's going to talk. In her memoirs and/or in interviews, she comes out against the tribunal and its unconstitutional nature - maybe in time to ruin Edwin Stanton during Johnson's replacement attempt with Grant. With Grant as SOW for the remainder of Johnson's presidency, I expect a much worse Reconstruction. Johnson and Grant were both the largest contributors to its initial and nearly half a century long failure. Stanton wanted to punish the conspirators...
...Johnson and Grant wanted to punish the South.
This is massive butterflies here, I realize. Not much would probably change. I don't think a civil court would let her free. I also doubt that they would have hanged her. So she lives, but in prison or exile. The abolition of military tribunals for civilians would come about sooner, probably, however.