Intern at 3 different companies within/supporting Fortune 500 companies, including automotive, financial, and educational fields. Collaborative Pianist for undergrad music students. Learning iOS development because it's awesome!
I have intern for a company that sees a lot of developers for projects, along with a different company that was very strict with VPN access.
First of all: contract, contract, contract. Non-compete and NDA at the least. We can have all of the security protection in the world, but if you don't put in legal writing that the IP and any code that you write for the project belongs to them (including anything written on the machine you provide), then there's no legal bounds for stealing the code.
One common way is to minimize local files on the computer; if an employee steals the computer, all of the files could be there. Host that on a secure server with authentication. You can also add another layer of protection with VPN access to the server. Doing this, you don't have public access to the server that hosts your code. Hard drive encryption also protects the employee and yourself from theft; even if the computer is stolen, BitLocker will render that data useless when the thief tries to take the laptop out the computer.
There are many many other mechanisms you can have in place, but that should get you started about the mindset you'll need to protect your source code.