Napoleon wanted an aligned Russia cooperative with his Continental System, not a broken Russia ravaged by ethnic strife & class war. 
French takeover of Lithuania was initially celebrated by the Polish & Lithuanian locals, but his refusal to restore Kingdom of Poland quickly soured them on the French. Loyalty to Russia in Lithuania was non-existent.
Despite brutal discipline, Napoleon’s troops were short on food & ravaged Lithuania. Tens of thousands of deserters left the army, preying on civilians & even French administrators & mailmen.
The Russian territories that Napoleon passed through prior to entering Russia proper (Smolensk) had few Russians or Orthodox Christians. Most people there were indifferent to both Napoleon & the Tsar. Many serfs took the opportunity to flee to freedom in the chaos.
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