r48: Ummm, I could not find any evidence that the war was the reason Van Johnson withdrew from the film.
Interesting tidbits from the web:
Gil Stratton, who had appeared in Girl Crazy, was originally cast as Judy Garland’s love interest. However, his service in the United States Army Air Corps kept him from the role. Van Johnson then accepted the role, only to drop out later (though he starred beside Garland later in In the Good Old Summertime). Robert Walker was considered, but Tom Drake got the part.
New York Times: HOLLYWOOD, Calif., April 22 1943 — Van Johnson, who was recently injured in an automobile accident and is expected to return to Metro-Goldwyn-Mayer within two weeks to complete his role in "A Guy Named Joe," will play the lead in "Meet Me in St. Louis," with Judy Garland.
From the AFI catalogue:
According to the Hollywood Reporter (HR), Paramount Pictures competed with M-G-M for the screen rights to Benson's popular stories. William Ludwig, and Victor Heerman and Sarah Y. Mason, who won Academy Awards for their 1933 version of Little Women, also worked on early drafts of the script, which, according to modern sources, included a kidnapping/blackmail plot line. Modern sources also note that while producer Arthur Freed was particularly anxious to make the film, Judy Garland, who was reluctant to return to teenage parts after successful appearances in adult roles in For Me and My Gal and Presenting Lily Mars, had to be persuaded by studio head Louis B. Mayer. George Cukor, who directed the 1933 version of Little Women, was first hired to direct the picture, according to modern sources, but bowed out after he was drafted into the Army. In Sep 1943, HR announced that Van Johnson had been cast in the lead male role. Robert Walker was also mentioned in news items as a cast member, and Gloria De Haven is listed in both news items and HR production charts as a cast member, but neither performer appeared in the final film. Lucille Bremer, a former New York nightclub singer, and Henry H. Daniels, Jr., a former tennis star, made their screen acting debuts in the film. Ruthe Brady , Tommy Batten, Wells Wohlwend, Joyce Tucker, Mickey Roth and Pamela Britton are listed as cast members in HR news items, but their participation in the final film has not been confirmed. According to HR new items, Freed "returned" to his former career as a songwriter to write the lyrics for "You and I" with his frequent collaborator, Nacio Herb Brown. "Boys and Girls Like You and Me," a song that was dropped from the 1942 Richard Rodgers and Oscar Hammerstein II musical Oklahoma, was shot for Meet Me in St. Louis, but cut from the final film. According to modern sources, the song, which was sung by Garland after the trolley scene, was removed at the insistence of Freed, who felt that it slowed the story. Meet Me in St. Louis was the first film on which Lemuel Ayers, who was the set designer on the Broadway production of Oklahoma, worked as an art director. Modern sources add the following information about the production: Although M-G-M wanted to use its "Hardy family" street set for the film, art director Jack Martin Smith and director Vincente Minnelli convinced the studio to build an entirely new set, which cost a significant $208,275. Most of the fair set was shot with miniatures, including two bisons sculpted by Henry Greutart. Principal photography went over schedule partially because of the many illnesses of the cast, as well as Garland's frequent absences and lateness. Lela Simone, a former recording pianist at M-G-M, worked as a music sound cutter on the film, and Dottie Ponedel was assigned as Garland's personal makeup artist. Ponedel, who changed Garland's onscreen look for the picture, became her regular makeup artist for the remainder of her career at M-G-M. The final cost of the picture was over $1,500,000. During its initial release, it grossed $7,566,000.