Why this is even a debate is beyond me. You pick Harbaugh every day of the week unless you are so insecure as a man that it isn't good enough for you to take credit for hiring the right coach and getting out of his way, you must be like Jerry Jones and prove you can win with anybody.
Jed York needs to learn from his uncle and from history - the coach with the right system will find the players to excel in that system. A GM with a great eye for talent will not be effective if he is constantly changing coaches and systems. Yes, the top 15 players on your roster may be awesome in any system. But the other 35 players may be worthless under a new coach and new system. Harbaugh has a proven system. Let him find the players to maximize it.
Eddie D. gave the franchise to Bill Walsh. The Giants gave the franchise to Bill Parcells. The Patriots gave the franchise to Belichick. You think Walsh, Parcells, and Belichick were universally loved by all of their players and front office personnel? You think Eddie or Bob Kraft would ship out Walsh or Belichick in favor of some former scout turned personnel executive?
Harbaugh is controversial and may rub people the wrong way - so get rid of those players and personnel that don't like him and fill the voids with Harbaugh's guys.
Baalke is entirely overrated. He gets credit for A. Smith (at the time a "reach" at No. 7) and Bowman (3rd Round, All-Pro) as far as I'm concerned. Drafting two first round graded OL in 2010 when our biggest need was OL was not genius. 2012 was entirely worthless. P. Willis, Gore, V. Davis, Staley, J. Smith, McDonald, Crabtree ... all here before Baalke got started. 2013 may prove to be a great draft if Carradine and Lattimore become studs, but part of me would have rather had two more high draft picks actually playing in the NFC Championship game versus sitting on the bench holding up "2014 signs"