Measuring how "out-of-order" an array is

Looks like what you are doing is essentially counting the number of pairs of elements that are in the incorrect relative order (i.e. number of inversions). This can be done in O(n*log(n)) by using the same idea as merge sort. As you merge, you just count the number of elements that are in the left list but should have been on the right list (and vice versa).

If the range of your numbers is small enough, the fastest algorithm I can think of is one that uses Fenwick Trees. Essentially just iterate through the list and query the Fenwick Tree for how many elements are before it, then insert the number into the tree. This will answer your question in O(nlogm), where n is the size of your list and m is your largest integer.

If you don't have a reasonable range on your integers (or you want to conserve space) MAK's solution is pretty damn elegant, so use that :)