No way I would choose the GM over Harbaurgh if it was my decision.
A GM's impact is completely over-rated IMO. Good coaches can make bad draft picks solid and solid draft choices good. A bad coach can make a good draft pick turn out poorly. When you find a coach with the track record of Harbaugh, you don't give that up. He helped completely turn around a failed QB's career (Smith) and took one of the largest draft project QB there was (Kaep) and had him leading them to a SB in year 2. And before that he helped develop the most NFL ready QB prospect the NFL has ever seen and might ever see again (Luck). This guy has the magic touch at the league's most important position.
None of that has anything to do with the GM IMO. Not even Kaep...the guy drafted a QB with a busted throwing motion who played in a pistol in college. You could draft 100 prospects like Kaep and give them to your average HC in this league and 99 times it isn't going to work out.