It will be interesting to see if they tear the entire thing down or incorporate it somehow. From the artists' conceptions, you can't see a big tree but it may be hidden behind the owl's wing in the photo.
I don't know if you've read/seen HP at all, but there is a tree involved in the books. It's called the Whomping Willow.. so a tree might make an appearance. It connects the Hogwarts grounds with the Shrieking Shack in Hogsmeade. It might not end up being a restaurant, but I couldn't see them leaving the Willow out of Hogwarts, so a tree will be around!