Good read on the situation. Did Marino and Harbaugh have any kind of relationship when they were both in the league together?
Not directly that I know, beyond being division rivals who were both tough guys and ****y guys.
However, if you'll follow me for a minute, consider this. Jim Harbaugh last played in the NFL in 2001, for the Carolina Panthers. This is probably where he met Greg Roman -- currently the 49ers' offensive coordinator (and before that Stanford's offensive coordinator) -- who was then an offensive line assistant. Roman had been hired while Dom Capers was the head coach of the Panthers, and after the 2001 season (after which Harbaugh himself was released), Roman left (was fired, more than likely) for the Houston Texans, who were then being coached by, you guessed it, Dom Capers. This same Houston Texans staff Roman joined included none other than Vic Fangio, who is currently the defensive coordinator of the 49ers (and before that, Stanford's defensive coordinator).
But really it goes back to Dom Capers. He hired Roman, and then Fangio. And who does Dom Capers lead back to? Bill Polian, who hired Capers to be the first head coach of the Panthers.
Are Polian and Marino close? That's hard to tell. But look at this:

If nothing else, Harbaugh is going to respect Marino, and he has an unbroken chain of personal recommendations leading back to him, from Roman/Fangio to Capers to Polian to Jim Kelly to Marino.