I would not call Napoleon a capitalist. His empire was based on the same foundations as the Soviet - military such - and there is obviously nothing wrong with that. This eventually led to the Napoleonic empire's downfall. However, many of the reforms Napoelon made, pointed towards clean socialism and certainly not anything else. Stalins Soviet Union had more in common with the bourgeoisin Western World of today than Napoleons military empire ever had.
However, I think Trotskij is really referring to Napoleon III when he speaks about Bonapartism. Under the first empire there was never such a political fraction as the Bonapartism. The Bonapartism was founded after the Napoleonic wars to get the emperor or his relatives back into power.
"Caesarism, or its bourgeois form, Bonapartism, enters the scene in those moments of history when the sharp struggle of two camps raises the state power, so to speak, above the nation, and guarantees it, in appearance, a complete independence of classes in reality, only the freedom necessary for a defense of the privileged. The Stalin regime, rising above a politically atomized society, resting upon a police and officers' corps, and allowing of no control whatever, is obviously a variation of Bonapartism—a Bonapartism of a new type not before seen in history.
Caesarism arose upon the basis of a slave society shaken by inward strife. Bonapartism is one of the political weapons of the capitalist regime in its critical period. Stalinism is a variety of the same system, but upon the basis of a workers' state torn by the antagonism between an organized and armed Soviet aristocracy and the unarmed toiling masses."
"The Revolution Betrayed"