Dear Aswathnarayana,

Electrical spoiling of port pin can damage other parts of chip too as other said. A small silicon damage can drastically bring down reliability and life of your micro.

There is no way to protect your code. If one has decided to steal it one way or other he will do it. Anyways the safest way to spoil a port pin in my opinion is Break apart the pin and apply some resin to seal the broken lead. You can use m-seal.

Regards,
Prahlad