Had McClellan won the election it still wouldn't have made a difference. In the first place, McClellan had backed away from his peace pledge during the campaign. And second, he would not have taken office until March 1865 anyway, so Lincoln would have pursed the war for a while yet. By March what was left of Lee's army was rotting away in Petersburg. Johnston is flailing away at Sherman who is near Savannah or else marching through South Carolina. The confederacy would still be on the ropes and not even McClellan would snatch defeat from the jaws of victory by giving the south what they wanted.
No, remember: just before the election, Lincoln wrote out a directive that stated that, once the election was over, he would follow the course selected by the electorate; that, if McClellan won, he would NOT push the enforcement of the war because he viewed that to be against what the people had decided in the election. To my memory (and I have to admit that I am working from memory here because all of my books are at home) he passed this directive around his cabinet as well so that they were aware of the fact that, should Lincoln lose the election, the direction of the prosecution of the war would change.
As far as the Johnston/Hood change of command, Sherman was worried more about a Confederate "army-in-being" staying in the local area of Atlanta, chewing up his rail-lines and interfering with his logistics, all the while sitting there like a rabid dog waiting to pounce on him should they be able to cut him off for very long. Sherman was relieved when Hood took over because he knew that Hood was the type of general to drive straight ahead (virtually, a Confederate Grant) and would not play the delaying game that Johnston had done so well. Sherman truly worried about and respected Johnston's ability in the defense. On a number of occasions during the Confederate retreat from Chattanooga to Atlanta, Johnston came within an inch of ambushing one of Sherman's columns and chewing it up, which would have gone a long way to equalizing the disparity of the forces.
A case in point is what Hood did with his Army once he got to Tennessee and Kentucky .. the battles of Franklin and Nashville displayed his utter incapacity to command such large forces or to make any plans other than the straight charge into the teeth of well-prepared defenses, bleeding the Army of Tennessee white at Franklin and completely destroying it at Nashville.
Sherman did not begin his March to the Sea until he was sure that Hood was headed for Tennessee and Kentucky, hoping that Sherman would follow him back in that direction. Sherman's statement (again from memory) was that, if he could be sure that Hood would go to Tennessee and Kentucky, he would give him the rations and the logistics train to do so; that General Thomas could worry about him instead of Hood hanging around the local area making foraging and resupply difficult, if not impossible.
Keeping Johnston wouldn't have automatically translated into keeping Atlanta; on the other hand, putting Hood in command virtually guaranteed that that would be impossible.