Web part deployment to farm solution

I've developed a Visual Studio web part for SP 2010 and about to deliver it the WSP file to the customer.  I understand that the SP administrator has to install it using PowerShell (is there any other way)?

How do I go about releasing the wsp file and protecting my code?  Will the SP Administrator ask to see the source code? 

Also the web.config file has to be edited.  What are the security and server disruption issues that need to be addressed when I request this to be done?  The SP server is a production server.

Thanks.