The average serf had no great loyalty to Russia or the Czar.
They took their Priests seriously, though. And the Russian Orthodox Church was one of the most xenophobic organisations on earth. To the average Russian Priest, Napoleon was an agent of Satan merely for being Catholic, never mind anything else about him.
This goes double, of course, when he's coming as the ally of the Poles, Russia's hereditary enemy from way back.
Perhaps Napoleon would find it easier to just carve Russia back into a series of individual principalities. Give local Russian nobles enough power to be able to squabble among themselves, plus a nice tribute bill to pay each year. The key thing, from his point of view, is that Russia must never be a threat again.
How does he get the power to do any carving? Even when he was occupying Moscow, did anyone make the slightest move to set up such a principality anywhere in Russia? And even if he leaves the whole Grand Armee in Russia (which he can't), it's still too small to occupy more than a fraction of the place.
I could imagine states of that kind set up on the Baltic, or in areas where the landowning (ie ruling) class included a lot of Poles, but all of that together is only a small fringe. Over 90% of Russia will be unaffected because he simply hasn't the physical power to dominate it. And it will be a threat again as soon as it get's its breath back.
If we're talking about the Russian army being mauled enough that it's a year or two longer before they turn the tide, well, maybe. But the idea that there could be anything permanent about it is surely ASB.