Apparently I didn't realise the fundamental error in my assumption which is that when dealing with arrays (or vectors in the case of MATLAB), I don't have default access to manipulating the pointers as would be in C. I have to deal with arrays by copying them around.
Edit: In case anyone is wondering what I ended up doing, it was something like this:
function [sortedA] = mergeSort(Arr, p, r)
if p < r
q = floor((p + r)/2);
leftArr = mergeSort(Arr(p:q));
rightArr = mergeSort(Arr(q+1:r));
sortedA = merge(leftArr, rightArr);