A data structure's form exists for one reason - to retrieve data. Don't look at what you want to store - look at what questions you want to ask. If you need to ask a lot of traversal questions, then store it as a tree (or, more generally, a graph). If you need to ask a lot of specific "What is your name?"-type questions, store it as an array of objects.

Furthermore, the way you store it on disk IS NOT the way you should handle it in RAM. How it is persisted in a permanent datastore and how you instantiate the data in your program are completely unrelated, save for the mapping between them. Storage on disk is marked by a paranoid avoidance of repetition. Storage in RAM, given that the disk is the ultimate arbiter, is more forgiving of repetition.

In other words, it's ok to load a bunch of data from the database, manipulate it a whole bunch, then use it. Just because the database views stuff one way doesn't mean you have to.