Leave the mission in to disrupt the trade ships, but instead just change it slightly. Instead of haveing the player SINK the trade ships, have them only destroy the enemy planes defending them. Maybe even go so far that if the player sinks a trade ship, he would be court marshelled. Once all of the enemy planes and boats protecting the convoy are destroyed, have some friendly navel ships, dock and board the helpless enemy ships, effectivly taking them over, and preventing the enemy from getting his goods.

Put some light defence on the cargo ships, such as a machine gun or something.

On a very cynical note: think of the publicity. If your game can stir up a controversy, then you''d probably increase your audience by a large factor. Normally you''d be paying large sums of money for publicity that most people would tune out. By being at the focus of a media storm (if you can manage it) you get free publicity that everyone will notice. There was a time a few years ago when if you asked a random person on the street to name a computer game, most people - and these are the ones who would have maybe played minesweeper a few times - would say "DOOM" because of the controversy about violent games and high school massacres.

I remember in Strike Commander (very old, but my favourite flight sim) you had to blow up a tanker in one mission, an oil rig in another and even a nuclear plant some time, but you were a ''good'' mercenary squadron and all the bad squadrons and governments you fought against, made you have no problem with doing what you had to.

If you really want to change it though, make it to destroy the convoy except those ships, to clear the way for the U.S. Navy to take over the freighters or something similiar?

Looking at it from a historical perspective:
What happened happened. The concentration-camps, the bombing of Hiroshima, the attack on the world trade center the 11:th amongst others, the wolfpacks in the baltics. Americans bombed convojs just as the nazi u-boats torpedoed theirs, all these things happened and I feel that there is no need to rewrite history just to please a few. The world was at war, countries bomb each other in war, that''s just the way it is and if your flightsim is under the WWII-era, then you should portray it just like it was.

Some will feel bad about what the americans did, but I guess some german players out there feel the same thing when a WWII-based shooter enters the market, but that doesn''t stop the products being made, does it?

On a more personal note:
While playing Battlefield 1942 over the internet, I experienced that some gamers out there has no qualms about gunning down players on their own team, just to get first to the airplanes so I don''t think they will have any problems bombing a bunch of AI-driven polygons traversing planes textures as water.
Think of that polygons poor children you just made fatherless, shame on you!

No, make your game as you''d like it. After all, it''s about war and in war people get''s hurt by bullets without being hit by guns.

As some Software company pointed out:
"Don''t make war, play war."