Well then you could put a script at the end of the template that looks something like the below example. You would have to put a class name on each of the A tags in order for it to loop through them. Might need to add some additional checking to prevent console errors but it should get you into the right ballpark:
<script>
var test = document.querySelectorAll('.CLASSNAME')
for (var i=0; i<test.length; i++){test[i]['href']=test[i]['href'].split('#')[0]}
</script>
There are some velocity helpers (substring, etc) though js would probably be a bit better.