Your adviser is correct. However, research design and methodology are always open to debate in the social sciences; methodological principles are more like best practices than objective rules, especially in qualitative research. Ask your adviser for citations to read on MDSD, but a couple books that might help: A Tale of Two Cultures by Geortz & Mahoney; Designing Social Inquiry by King Keohane & Verba; Rethinking Social Inquiry by Brady & Collier. Other authors/editors of methods books: Getting, Geddes, Yanoe & Schwartz-Shea. (I don't recall which ones discuss MDSD without referencing the books which is why I say ask your adviser.)