Of course, once we start optimizing how the original array is stored, we may have exceeded the limits of this problem as a teaching exercise :)
As for time, it does seem to be O(n) to me; can you clarify why you think it's nlogn? It may not be particularly fast in practice when compared to other O(n) approaches like the bitmap, but I don't think the complexity is wrong.
Your solution is nice - it actually gives you more information (how many appearances, not just T/F >1 appearance), but it does require more additional space and isn't necessarily faster. I think the bitmap approach would be nicer if you're ok with using more space; the bitmap is essentially a very easy to find perfect hash function due to the unique input constraints.