Why did the Alter Rebbe oppose Napoleon? In an 1812 letter to Rabbi Moshe Meiseles, head of the Alter Rebbe's spy ring that funneled information about Napoleon to the Tsar, the Alter Rebbe writes:
Should Napoleon be victorious, wealth among the Jews will be abundant and the glory of the children of Israel will be exalted. But the hearts of Israel will be separated and distanced from their Father in heaven. But if our master Alexander [the Tsar] will triumph, though poverty will be abundant and the glory of Israel will be humbled, the heart of Israel will be bound and joined with its Father in heaven.
The Alter Rebbe feared democracy and modernity. His decision to support the Tsar (if it was, in fact, helpful to the Tsar) led to 180 years of Jewish oppression and suffering, sparked the massive wave of emigration to the United States and accelerated assimilation. But, hey, that's okay – he was a tzaddik, right?
An academic treatment by Hillel Levine of the Alter Rebbe's opposition to Napoleon is found in Rachel Elior's book on Shabbatianism. Download hillel_levine.pdf
(Also see comments to this post for an earlier discussion of this topic.)