I agree (gasp) with Steve that your best bet would be to book open jaws into Frankfurt and out of Salzburg.
However, I think you should go by train from Salzburg to Frankfurt. By the time you get out to the Salzburg airport in plenty of time, fly to Berlin, wait for the connecting flight, and fly to Frankfurt, you'll probably take as much time as on the train. I see a 5h20m connection by ICEs through Munich, leaving Salzburg at 9:02.
If you commit to trains and book well in advance, you can get a Sparpreis fare as low as €49 for two people from Salzburg to FRA, or even to the Rhein.
If you are worried about retracing, I suggest you go a different route to Rothenburg. Take the train from Frankfurt to Mannheim, then go to Weikersheim (on the Romantic Road), via Heidelberg & Osterburken. There are buses from Weikersheim to Rothenburg. A single trip ticket will cover you from Mannheim Hbf to the Baden-Württemberg/Bayern border between Creglingen and Rothenburg, for €8,30 pP. A VRN "Ticket-24 Plus" is a Tageskarte (day ticket, €20) and will cover both of you on/off for 24 hours along that route, allowing you to stop in, say, Heidelberg on your way.
As for seeing the Rhein, AirBerlin flies directly to Cologne/Bonn, which is nearby.