Ehm.
The Rhinelanders were more then happy to be part of the French Empire, actually, and French had become popular among the young intellectuals there.
The issue was that for them, the primarily liberal, burgher-dominated lands had been ruled by conservative, aristocratic princes, and were now replaced by a liberal meritocracy. Where once they as a middle class were chafing under the arbitrary powers of the aristocracy, they now had freedom to partake in positions of power throughout the Empire, with liberal Imperial laws replacing that of the ancien regime. The socio-political structure of the Empire after Napoleon's reforms were highly attractive for many, as now they had an opportunity for advancement that had been so long denied to them. The Empire swept away the old, outmoded feudal system and brought new civil, legal, political, and administrative reforms to the region, which made them highly supportive of the French state, understanding that defeat or restoration of the Rhineland to their former masters would mean a return to feudalism and despotic aristocracy (which it did).
That´s too simplified I think.
I agree that the French revolutionary armies were welcomed in the Rhineland initially. The people were tired of the old "Middle Age" structures. The young intellectuals however were a tiny minority. The burgher dominated towns liked their new freedoms. Initially even the rural regions - where most of the population still lived - saw some improvements.
(Using churches as horse stables might not have been a good idea though.)
However almost two decades of almost constant war took their toll.
Think taxes and sons drafted into the French army year after year.
I´ve read that by the time of the Russian campaign in some regions (French) public servants needed an army escort going to farmer villages to draft sons into the army.
There´s also the fact that the mass armies introduced by the French revolutionary wars relied on "local supplies".
Which means that you - owning a house in a town - could be required to house maybe 2-4 French soldiers. Providing them with a bed and food.
Or if you were a farmer the French army could requisition x% of your harvest at pre-determined prices.
If it happens once or twice you probably grumble and then forget it. Two decades of warfare however will probably strain your patience.
(Not to mention that the Rhineland after 1815 wasn´t returned "to their former masters [which] would mean a return to feudalism and despotic aristocracy". Prussia had already introduced the "General state laws for the Prussian states" in 1794. And the Code Napoleon in his translated / germanized form stayed in power in the Prussian Rhine provinces.)
Indeed, the Rhinelanders were among Napoleon's most enthusiastic supporters, and even after 1815 were regarded by the Prussians with suspicion due to their Francophilic tendencies.
Any region being liberal and Catholic would have been viewed with suspicion by the Protestant Prussians. By 1815 I´m not sure if the Rhineland was still that francophilic / Napoleon enthusiastic. Two decades of war will wear down a lot of enthusiasm.
The whole "Rhinelanders speak German and thus cannot be assimilated" is not in and of itself a justifiable premise to call it ASB. Social identity is much more fluid then that, and OTL nationalist movements were the result of frustrated romanticism and liberalism in an era of a reactionary Metternichian framework, which stemmed from the "defeat" of liberalism and Enlightenment ideas (embodied by France). The nationalist movements, in an TL in which liberalism triumphs, say, with a surviving Empire or Empire turned Republic, would thus have to draw on different roots. With the continuation of a French Rhineland, the social and political reforms which bound the Empire together would drift the Rhinelanders towards a French identity. And honestly? With the economic center of France moving north and east, so too will French contemporary culture, so it's entirely possible to see a more "German" France.
Ehm.
The French revolutionary (citizen mass) armies "exported" revolutionary but also nationalist ideas. And as mentioned above two decades of taxes, housing and supplying French soldiers - not to mention getting your own sons drafted for wars in faraway European countries - tends to cool revolutionary enthusiasm somewhat.
Especially if the French Revolution creates the French Empire with Emperor Napoleon I, lots of newly created Kings and Dukes and whatever.
Throw in Joseph Fouché and I´m a bit puzzled why you think that the French Empire embodies liberalism and enlightenment?
Take Prussia as an example.
In 1806 the defeat of Prussian armies was met with shrugs by the Prussian population. In 1813 the situation had changed a lot.
I think if you want a French Rhineland you either need
- a victorious Napoleon in Russia or
- an end to the wars in 1804/06? Allowing France to slowly assimilate the Rhineland (peace and prosperity). Not an additional decade of warfare with Napoleon.