As has been mentioned you can happily submit a patch to the author to make the module return a reference to a hash, rather than the hash. If you think it's worth while, then perhaps other people will, and your patch will be a welcome addition.
You could also look at the plethora of other configuration file reading programs out there. There is no shortage, Apache style, Windows .ini style, XML or YAML format and dirt simple style. I'm sure you will find that some of them return their configuration data in hashref format.
... and more. There are plenty to choose from. Some I know for a fact return their configuration as hasrefs.
HTH, and Good Luck!