Gothampc, actually I always loved the way the scene and the song were lighted. Maybe I'm overthinking it, but the scenes within the office were indeed dark and "closed" like life in the Abbey itself would be. But when the Mother Abbess sings the song and looks out the window, we see how bright the rest of the world is. It just emphasizes why Maria NEEDS to leave the abbey and go out into that bright and sunny real world. The light on Peggy Wood's face still gives me the chills, not to mention the little spray from her mouth as she sings (or pretends to). Those office scenes were actually shot in a cover set which is why those scenes look darkly lit, etc.
Principal photography on the film began with location filming in Austria. Unfortunately, it rained quite a bit which extended location filming to 11 weeks. In order to take advantage of not wasting time, they had countless cover sets in case it rained, etc. Many intimate scenes in the film were shot in a cover set, including that Maria/Mother Abbess office scene, which was shot during rain breaks from the "Do Re Mi" filming.
Many people involved with the production commented that NOW they understood why Austria has those lush greens and foliage: IT RAINS ALL THE TIME!