Database administration site on Drupal: entities vs. manual programming
While I can't see any significant benefits to doing this with Drupal, I think this should generally work. I've converted old systems that were using db_query and custom code to Drupal 7 Entities with the Entity API module with success, and I've been pretty pleased with the results. As long as the schema is solid, without issues, or you can modify it as needed, this will work fine.

Depending on the data structures and the normalization of related entities/properties you may need to create your own EntityController to override the loading (and saving if using Entity API module) to ensure that the data is queried and updated properly.