I'm not a historian, but from what I remember reading, the North (and most of all, Lincoln) wanted to get the country back on track as soon as possible, with as little animosity as possible. Revenge or punishment was seen as being too disruptive to the future of the reunited nation. The thought was that the sooner the South was up and running again socially, politically and economically, the better off the entire country would be.

A great deal of this has to do with the terms of surrender at Appomattox. One of the terms offered by Grant was that the surrendered would be free to return to their homes "not to be disturbed by United States authority so long as they observe their paroles and the laws in force where they may reside."

This was extraordinarily generous, given the respective situation. But, IIRC, it was also in line with Lincoln's views to "let them up easy". In any case, it seems to have made the "hang Lee" feeling impossible in the North, because it would have been a slap in the face to US Grant, and, by extension, to the Army of the Potomac.

Didn't the confederate officer that ran Andersonville get brought to trial? I seem to remember that.

Ok I don't know how to edit but I was right http://en.m.wikipedia.org/wiki/Henry_Wirz Tried and executed

I've also read quite a few times that union commanders were particularly worried about a protracted guerilla war with remnants of the confederate army. Nathan Bedford-Forest being the prime example of someone who might (and eventually did with the KKK) be moved to continue the fight in the dense Appalachian region. Executing former confederate officials would have played into the deepest fears of these more radical elements and could have perhaps insighted such a conflict.