Hey
Sorry but I don't understand this answer. I too like to hear reasons for decisions to stay away from non-relational databases.
Your first point, that you'll be using JSON, feels strange. When I build stuff, the data storage and the usage of the data are very separate areas. The web part using the JSON doesn't know or give a damn if the data is stored in MySQL or MongoDB or written in sand and translated to computer-speak by monkeys.
Second - Maybe I'm misunderstanding you, but isn't this tree structure a number of entities that have relationships with other entities (as parent / child / sibling / whatever). How is that not applicable to a relational database?