In general, what penalty do you provide to an employee that takes company Intellectual Property away (violating the non-disclosure agreement)?
What is the best way to protect our bigger value (source code)?
If you can't come to agreement with the person who took your IP the only recourse may be for both of you to make some lawyers a little richer. The best thing to do is not to hire people you can't trust.
Having said that I have stored some very proprietary source code in a library that was stored in version control with the rest of the source, but only highly trusted employees (3 in addition to myself) had access to that module. The binary for the library is distributed with the application and is available to anyone in the company, but access to the source is very closely guarded.
You have to decide whether it's worth going after him in court. In the US, you'd probably have good claims for breach of contract, misappropriation of trade secrets and copyright infringment. In Italy.... Well, see a lawyer.
As to 'how to protect' the code . . . Hire people you trust, do background checks if appropriate, and then use internal controls to segment the code that individuals are allowed to look at.