That Napoleon would sacrifice good will in the conquered non-French zones in order to favor the French core is all too predictable of course; it might have been superhuman of him to do otherwise. One does not have to be a total Utopian to imagine him taking advice to balance the Continental System as a step toward imperial consolidation, since it would be in his interest to spread the sentiment that his Empire was about more than the welfare of France, as the Emperor of all--more glory for him, and after all as a Frenchman he was peripheral, from Corsica--he just might empathize with people whom the French consider foreign, a little bit anyway. Of course it often doesn't work that way; though Stalin never lost his Georgian accent, the longer he held power in the USSR the more he wanted to be accepted as Russian and the less indulgence he gave the non-Russian Soviet citizens; I don't know if Napoleon suffered a similar passion to be accepted as French.
Stalin didn't roll back the minority privileges out of personal enthusiasm for the idea, he did it out of realpolitik in order to remain in power.
The Soviets had offered a huge amount of privileges and concessions to non-Russians within the Soviet Union; to large bodies like the Ukraine and Armenia that had seriously attempted secession, to tiny minorities in obscure corners of the CCCP, and to dispersed groups like the Jews. Special regions were carved out. They even began a process of using latin letters to instill literacy in the minorities. The only thing completely out of bounds was religion, and there the stance tended to be more lenient than for Orthodox Russians.
Russian national feeling had also been suppressed. Simultaneously, the Party recruited and exalted factory workers and peasants who were unsympathetic to rebels, hadn't heard of and didn't care about most small groups, and actively disliked the Jews (if not the Germans). Workers and peasants who were mostly ethnic Russians.
Stalin's later policies were simply a reflection of the fact that the only group he actually needed on his side to stay in power felt aggrieved. If he'd been ethnic Russian perhaps he could have gotten away with it, but as a Georgian he was desperately at risk of being seen to be too soft on the minorities. It was an "only Nixon can go to China" situation.
It is still a heck of a homework assignment trying to figure out a plausible sequence of events to lead to that.
I suspect all you really need to end the cycle of coalitions is to have Napoleon die between 1807 and early 1812. There were so many problems on France's plate that, with the addition of politicking around the throne, it's pretty safe to assume Bonaparte's adventures are avoided. But by that point France's position was so strong that there's no credible challenge to be raised to its dominance over Europe.
Keep the French focused close to home for a decade, only mustering the incredible strength at their disposal to maintain what Napoleon built, and deny their enemies the specter of Napoleon and the opportunity of Russia. I suspect that'd be all it would take.
Certainly there would still be wars, but without the momentum for expansion Napoleon leant his empire (or the way he rallied his enemies against him), peace is likely to break out in which France can't help but consolidate within the borders it has drawn.