With the Civilization series being one of the most succesful on the market and known by most gamers, bringing Hitler as one of Germany's playable leader would bring a lot of controversy. It's not risky to allow the player to play as the Germans during WW2, but it's risky to allow the player to play Hitler himself.
There are some games that allow you to. The Hearts of Iron series allows you to play as Germany during WW2 and, as such, Hitler. But this series is not well known amongst most gamers and is aimed at historians and players who love
strategy games over arcade action.
As for Stalin in Civilization. He's a victor, so we don't talk too much about how much of a bastard he was to his own people. Hitler lost the war, so he's seen as a worse person than Stalin.
Besides Stalin is such an excellent leader in Ciivilization IV! I always take him when I want to wage war.
Another note for Civlization. The game spans across all ages. The game takes the most influential leaders of the nation's history. Those who, by one way or another, brought their civilization to glory and power. Bismark is much, much more important as to what Germany is today than Hitler.