I dont think you need to tweak ember for that. Simple solution is before ember application loads you can run the following code.
var url = window.location.toString();
if(url.split('#!').length==1) {
if(url.split('#').length==2) {
window.location = url.split('#')[0]+'#!' + url.split('#')[1];
}
}
Basically what it does is rewrites the url to #!.
UPDATE: Else one more way is write above code in Ember Initializers.
Here is the jsbin http://emberjs.jsbin.com/aLiretO/1#post