This is, of course, conjecture. However, of the two options, I would argue that the absence of these men would have made the war drag out longer but would not have caused the South to win. The reason I say this is that the decisive advantages that the North had would not have gone away if those men had not been put in important positions.
The Union won, in my view, for three reasons. First, it had huge material advantages due to its manufacturing base and the South's lack thereof. Second, it had the stronger hand politically, given that the European countries were not likely to recognize the South's independence, particularly after the Emancipation Proclamation. Finally, the North won because of Abraham Lincoln's leadership. It seems likely that he would have continued to look until he found generals who would be aggressive enough to suit him.
Now, it is always possible that things would have turned out differently. Perhaps there would have been no victories in late 1864 to allow Lincoln to be reelected. If McClellan had won that election, the war might have been over even if Lincoln would eventually have been able to win it given time.
On the whole, though, I would argue that the absence of these three men would not have doomed the Union.