If I remember correctly, if Napoleon has a lot of cities (spam or otherwise), you capturing a few of them won't put much of a dent in your warmonger status. It is when you go for his core cities, that it usually amps up.
In a recent game as America, Japan was city spamming and also conquered a lot of French land and taking Moscow. I was friendly with most of the civs and denounced him, followed by everyone else. Now when I went and took all but 2 of his cities and liberated Moscow, I never had more than a "minor" hit to my warmonger status. This is also due to Carthage, Venice and Byzantium joining in the war with me.
I razed 2 of his little perimeter cities. Kept one to move my B17s closer and kept 4 of his bigger ones as puppets. It was late game, so I never bothered to annex. My war with Germany left me with Berlin and Cologne in an earlier war...those eventually became annexed. I try to annex capitals once they get back on their feet a bit.