Honestly, I don't entirely blame Jeunet for being (to say the least) trepidatious, Amelie is such an anxious, claustrophobic film that really lives in its medium - this is that question of, like, what medium best serves the story? Are they going to improve on the film by musicalizing it? Not that I'm not curious but I don't think his reaction is so unexpected (also, though I know it would draw Sweeney and probably Urinetown comparisons, Delicatessen seems way more musicalizable).
Unsure about Amelie (a film I really like) as a stage production, but perhaps really great projection could fill in for the quirky cinematic close-ups that are an integral part of the movie.