First I have to say it looks pretty good for a 9-year-old's room. Is there any other wall on which the loft bed will fit? The wall between the entry and the closet, perhaps? The most disturbing thing to me is that it hangs over the window. If it has to stay there, I would look for ways to eliminate the legs in front of the window. Perhaps you could build a platform and have the end of the bed cantilever. Or hang the whole thing from the ceiling joists.

If you could suspend the bed, it would get rid of all the legs and you could put shelves behind and to the right of his desk. In the pictures below, they used some kind of rope, but I think aircraft cable would look cool.