Two notes before I give my two cents:
1) The arrangement between Cologne and the Arch-Bishopric of Cologne was that the city itself had successfully revolted against church rule, which led to the bishop establishing himself in Bonn instead. Fun fact, the university in Bonn is mostly located in the former palace of the archbishop! But yes, it was not uncommon for ecclesiastic states in the HRE to be named after cities they didn't control. The Prince-Bishopric of Lübeck is another example of this, though since 1586 it had been under a Lutheran administration...
2) Actually Hessen-Kassel was the main beneficiary of the end of the Grand Duchy of Frankfurt. Here are a few maps provided by the Landesgeschichtliches Informationssystem Hessen that nicely showcase what the region looked like from 1789 to 1821.
1789 - Pre-Revolution | 1803 - After the French annextion of the Rhineland | 1807 - After the formation of the Rheinbund | 1812 - The Grand Duchy of Frankfurt at its greatest extent | 1821 - After the restoration of the old order
Now, given this information, I do think that it'd be quite easy to give Beauharnais the former Grand Duchy of Frankfurt and the Principality of Isenburg, or most of it. These territories were very much in flux during that era and with his history in the region, Eugène would honestly be a legitimate candidate. The question that arises then is the matter of compensation. And for that one can, knowing how the Congress of Vienna worked, do a bunch of horse trading!
For one, as mentioned, most of these lands actually went to Hessen-Kassel, which had ceased to exist and was fully subsumed into the Kingdom of Westphalia. Certain territories, such as the city of Hanau, even were part of Hessen-Kassel before the war. Still, it's not like all of Hessen-Kassel's former territories were returned to them, e.g. Katzenelnbogen, which went to Nassau. So one could easily have Kassel regain Katzenelnbogen in whole or in part as an exclave as part of their compensation. Nassau in return could keep, or rather regain, the Siegerland (which went to Prussian Westphalia IOTL) or larger parts of what would become the post-war Prussian exclave districts of Braunfels and Wetzlar (after 1822 just Wetzlar, as both were merged). Also Kassel didn't mind exclaves, though they did sell most of their northern exclaves to Hannover not long after the Congress, but they did keep Schmalkalden and their part of Schaumburg until their very end. So keeping Katzenelnbogen seems very doable.
Wetzlar's environs might also provide good compensation for Hessen-Darmstadt, since it might be made to part with some of their possessions. Amt Itter, the exclaves bordering/inside Waldeck-Pyrmont would be an excellent choice, since it was under joint rule by Darmstadt and Kassel in the 17th century. Still, if Hessen-Darmstadt were to gain/keep Mainz and partition Isenburg along similar lines as it did IOTL with Hessen-Kassel, it may just be fine "as is", because Mainz was still up in the air during the Congress of Vienna, and Aschaffenburg, too. Another option for a possession Darmstadt could keep is (Sayn-)Wittgenstein, which it did gain in 1806 but ceded to Prussian Westphalia in 1815. It was a pretty poor region, but hey, minor states can't be that choosers.
The big problem, in my personal opinion, is how to get Bavaria on board. They had designs on the region, hoping to establish a big stretch of land covering cities like Aschaffenburg, Frankfurt, Fulda, Hanau, Heidelberg, Mannheim, and potentially Landau, Mainz, and Speyer, directly connected to Franconia and thus their core in Altbayern. Ideally all while keeping parts of their gains made at Austria's expense, such as Salzburg.
Bavaria would likely protest a bit too much if Aschaffenburg was taken away from them, but if they could still get Aschaffenburg and maybe get a more favorable division of the former Principalities of Hanau and Aschaffenburg, then OTL arrangements could still work out (as in Austria gets Salzburg and Bavaria establishes their post-1816 Pfalz in west of the Rhine).
Wetzlar itself however seems very unlikely to be given to Beauharnais again. It was an important fortress city and Prussia was intent on using it as part of their duty to defend the Rhineland, so giving that up seems unlikely unless they would get compensated elsewhere, such as what would become OTL's Bavarian Rheinpfalz possibly also including Mainz, or more of Saxony in the east. A smaller Kreis Wetzlar is very plausible, but yeah... There were three important cities for the defense of the Rhineland in the region, Frankfurt, Mainz, and Wetzlar, and Prussia will insist on controlling one directly and having access to at least a second one, otherwise its role as protector of the Rhineland would be in jeopardy.
Also, last but not least, the city of Frankfurt itself. Beauharnais may as well actually get it, as long as Prussia, Austria, and Bavaria gain the right to station troops there. But if he doesn't, maybe his grand duchy might get renamed, or it might not. Grand Duchy of Fulda doesn't sound bad either as a name, or Grand Duchy of Aschaffenburg in case he gets to keep that city.