They used a security hole of an open command at index.pl this to be exact.

No, they did not. They used a security hole in your program, not a security hole of the open command.

Should i have to be considered responsible for such an action?

In a way yes. Normal people are responsible for their own actions. That doesn't mean you are the only one to blame though. The people who gave you the ability to upload scripts like that are also to blame. Whether you are liable for damages depends on what kind of contract you have with the company.

Next time, use tainting.

Abigail