In the end I did what I mentioned at the end of my question. Added this bit of inline JS prior to the call to the history plugin js file:
(function(){
if (document.location.hash.length !== 0) {
document.location.hash = '';
}
})();
At worst we end up with the URL still having a trailing #
at the end, but as it doesn't have #/
then the history plugin doesn't then mess it up.