Binary search vs binary search tree
Note also that there are standard algorithms for maintaining balanced binary search trees. They get rid of the deficiencies in binary trees and maintain all of the other strengths. They are complicated, though, so you should learn about binary trees first.
Beyond that, the big-O may be the same, but the constants aren't always. With binary trees if you store the data correctly, you can get very good use of caching at multiple levels. The result is that if you are doing a lot of querying, most of your work stays inside of CPU cache which greatly speeds things up. This is particularly true if you are careful in how you structure your tree. See http://blogs.msdn.com/b/devdev/archive/2007/06/12/cache-oblivious-data-structures.aspx for an example of how clever layout of the tree can improve performance greatly. An array that you do a binary search of does not permit any such tricks to be used.
There's not much of a benefit in querying either one.
But constructing a sorted tree is a lot faster than constructing a sorted array, when you're adding elements one at a time. So there's no point in converting it to an array when you're done.
Your analysis is wrong, both insertion and deletion is O(n) for a sorted array, because you have to physically move the data to make space for the insertion or compress it to cover up the deleted item.
Oh and the worst case for completely unbalanced binary search trees is O(n), not O(logn).