Very good points.The problem is that some states which McClellan absolutely had to carry--notably Illinois and Indiana--did not allow soldiers to vote by absentee ballot--yet Lincoln carried these states anyway (and neither Illinois nor Indiana was super-close).
"The close election demanded attention to every political constituency, especially the Union soldiers. Each individual state determined on their own the process by which soldiers' vote was to be handled. Wisconsin was the first to permit their soldiers to vote in the field through absentee ballots. California, Connecticut, Iowa, Kansas, Kentucky, Maine, Maryland, Massachusetts, Michigan, Minnesota, Missouri, New Hampshire, New York, Ohio, and Pennsylvania all followed suit. However, Illinois, Indiana, and New Jersey, which all had Democratic-controlled state legislatures, did not pass legislation allowing soldiers to vote in the field. Likewise Delaware, Rhode Island, Nevada, and Oregon failed to permit absentee voting. Whenever possible in these cases, soldiers were granted leave so that they could return home to vote." http://www.nps.gov/liho/learn/historyculture/lincolngrant.htm
IMO Illinois is the state posing the greatest single obstacle to a McClellan victory. Yes, it had elected a Democratic legislature in 1862. But already in June 1863--*before* Gettysburg and Vicksburg--it voted to reject the "Copperhead Constitution" "by a margin of 24,515 votes." http://www.lib.niu.edu/1996/iht319615.html In 1864 its margin for Lincoln was substantial (54.4-45.6) and as noted, was produced *without* any absentee soldier vote. And without Illinois, I just don't see how McClellan wins.
There was an informal policy of letting as many Indiana soldiers as could be spared go home on leave over the election - without that, there might have been a difference. But, as you say, Illinois. And I'm really grasping at this point. You're right; refusing absentee ballots alone wouldn't make a difference.