I think it deeply depends on how much variation in code is actually there to support the database(s). Along with how much data, how many collections, and how would you handle the migration and/or scaling with your proposed alternative? Is it worth stopping all feature development for weeks/months to migrate? How profit driven or constrained are you?

There's a lot that I like and dislike with MongoDB. As a developer, it can be a relatively nice experience. As an administrator, I hate it beyond words. It really depends on your needs, entrenchment and the skills of your staff.