As noted in the comments already, there seems to be no way (yet?) to get the path itself without a regex. So this is the only way to go:
Basic solution
FileDialog {
    onAccepted: {
        var path = myFileDialog.fileUrl.toString();
        // remove prefixed "file:///"
        path = path.replace(/^(file:\/{3})/,"");
        // unescape html codes like '%23' for '#'
        cleanPath = decodeURIComponent(path);
        console.log(cleanPath)
    }
}
This regex should be quite robust as it only removes the file:/// from the beginning of the string.
You will also need to unescape some HTML characters (if the file name contains e.g. the hash #, this would be returned as %23. We decode this by using the JavaScript function decodeURIComponent()).
Fully featured example
If you not only want to filter the file:/// but also qrc:// and http://, you can use this RegEx:
^(file:\/{3})|(qrc:\/{2})|(http:\/{2})
So the new, complete code would be:
FileDialog {
    onAccepted: {
        var path = myFileDialog.fileUrl.toString();
        // remove prefixed "file:///"
        path= path.replace(/^(file:\/{3})|(qrc:\/{2})|(http:\/{2})/,"");
        // unescape html codes like '%23' for '#'
        cleanPath = decodeURIComponent(path);
        console.log(cleanPath)
    }
}
This is a good playground for RegEx'es: http://regex101.com/r/zC1nD5/1