Honestly, I've been thinking that, too - as in "Is Reds1 going to kill off one (or more) of his players serving in WWII?"
The reality is, two major leaguers did die in World War II. Neither were known for their exploits on the diamond (both had cups of coffee in the bigs in 1939 and had been back in the minors for a few years before they enlisted) but when it came to their service, both were well-accomplished. One (Elmer Gedeon) was a bomber pilot, and the other (Harry O'Neill) was a decorated Marine who served in the Pacific and was killed at Iwo Jima.
Ultimately, it's up to you. Maybe choose one player to make the ultimate sacrifice, then find some way in the league structure to honor him, be it an award, or a stadium named in his honor, or some sort. Or you could have a player come back injured, unable to play anymore, but still serve as a coach or general manager (a la Bill Veeck).
Just as long as it isn't Finley Capstick