Split of Habsburg Lands
A German unification wound not necessarily mean an end to Habsburg rule in either Austria or Hungary. The easyest way for the Habsburg to continue to rule both countries would be devolution. The Hannovarians until the death of William IV. were both Kings of the United Kingdom and of Hannover. If that would not be enough, the Habsburgs might choose to split their House as they had done it before, when the lines of the spanish and austrian Habsburgs seperated.
Let's say, that Ferdinand, called the benign does not resign December, 2nd 1848 and would still be austrian Emperor by the time the Paulskirchen Constitution is signed. Since the Hungarians demand a complete Seperation from Austria, he resigns in favour of his two nephews Franz-Joseph and Maximilian (who will then not be offered to become emperor of Mexico by the grace of Napoleon III.) to rule in Austria and Hungary respectively as constitutional monarchs. Thus Austria, that most probably would become a Kingdom (since it would be absurd to have an austrian emperor within a united Germany), uniting the multiple archduchies, could join Germany. The demands in Bohemia and Moravia for a panslavistic solution could be countered by a devolution of the Habsburg holdings within the German Empire.
To make german unification more acceptible for the Habsburgs, the imperial crown could alternately be bestowed to the King of Prussia and the King of Austria. (There was in fact a proposal in OTL in 1871, that the imperial crown should be bestowed alternately to the King of Prussia and the King of Bavaria to make the german unification under the King of Prussia more digestible for the Bavarians, who had only 5 years earlier lost a war against the Prussians, but this was turned down by Bismarck, who already had enough problems to persuade Wilhelm I. to accept the title of "German Emperor" - in fact Wilhelm, who favoured the title "Emperor of Germany", did not accept it until considerabely after the proclamation, where the grand-duke of Baden simply chose to proclaim "Long live Emperor Wilhelm", thus avoiding the dispute between the King and Bismarck.)