Calling Apex Metadata API from Post Install Script: Actually calling the metadata API from an Apex Post Install script is going to be problematic, since in order to call the Metadata API (which is a web service) you need to setup a Remote Site setting the customer org to permit the outbound call (which ironically is back to Salesforce servers). While you can package Remote Site settings you probably don't want to include one for every possible Salesforce instance your package can be installed on.
Alternative to Automating Post Install Task via Apex Metadata API. If you want to call the Metadata API post install, i would recommend providing a short post install process, to add the appropriate remote site, then have the admin navigate to a Visualforce page which contains any required post install org configuration changes you want to automate. You could use the Package Configuration link (see package definition) for this perhaps.