If I had to choose between Saban and John Harbaugh I might lean towards Harbaugh. His age and success at the NFL level are second to none. And his biggest question mark would be recruiting, but he has a pretty good resource in his brother to help him get that worked out.
To me, I'll ALWAYS choose a coach who has been successful in the NFL over a guy who has only had college success. Saban makes the idea more complicated, but think about it this way. In the NFL, more often than not the teams on the field are relatively equal in talent. Every player on the field is a certified badass. Coaching plays a MUCH greater role in determining the winners and losers in the NFL than in college. In college, talent might be comparable 2-3 times a season between teams. In the NFL, you might have more talent than your opponent 2-3 times total. Consider that Harbaugh has won a Super Bowl, there's absolutely no argument to the question on whether or not he can coach.
Think about this. Before Pete Carroll got his second shot and Jim Harbaugh took over the 49ers, the good to great college coaches who went to the NFL were flame outs. Nick Saban, Steve Spurrier, Bobby Petrino, Mike Riley, Dennis Erickson just to name a few. And three of those coaches won national titles before taking on the NFL. There are a LOT more guys who have had success coming from the NFL to college than vice versa.
The best thing about Harbaugh is that he's a players coach. I can remember a number of articles last year about Baltimore's run where they talked about how the team was struggling and Harbaugh got his veterans like Lewis and Reed together to figure out what needed to be changed. They said part of it was him. He took the criticism and changed himself and ended up making a run straight to the title. That's the kind of thing that you want to see from a guy with NFL ties coming to college. With the right staff around him of guys with strong recruiting backgrounds he could be a homerun.
One last thought. The most difficult thing about the NFL is the competitive balance structure in the league. Between the salary cap and draft it's nearly impossible to completely load up on talent. You don't have those kinds of issues in college. The only limitation is the 25-85 scholarship rule. But if you can be like Saban and sign top ranked classes every year you can enter just about every game you play with the talent advantage. And couple the talent advantage with the fact that Harbaugh or anyone from the NFL would more than likely be the best coach on the field each week and you have a recipe for domination.