You have to pass the array not the address of the array to qsort.
qsort( output, ... );
Also your compare function must return an int and accept two const void* arguments.
Casting your function int compare (words *a, words *b)
to a different( yet correct ) type which is then called by qsort() will cause undefined behaviour.
The compare function must be:
int compare (const void *a, const void *b)...
Then you cast a and b to correct types:
((words*)a)->hitCount < ((words*)b)->hitCount