If you wanted to do it through a metadata deployment, your only option would be to delete the old class and create a new one.
In the ui (Setup > Develop > Apex Classes), you can change the class name, but it won't change any of the references, so if you don't manually change all references to the class, you might start getting errors that say:
Dependent class is invalid and needs recompilation
Renaming a class in the ui will associate a different name with the same salesforce id for the class, so there is a subtle difference between that and deleting and creating a new class.
Hope this helps!
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