All creative works, including code, are protected by copyright the moment they are created. The protections of copyrighting are limited though, and at the time he was caught Mr. Aleynikov had not done anything other than copy the code. There was no distribution to other parties and no sale of the code, which meant there were limited damages. In other words, if they went after just copyright then there was no real difference between this guy stealing a font or stealing the software itself- the punishment would have been minimal at best. Because of this the focus was placed on trade secrets, and of course that failed to work due to the reasons the article addressed.

The code became copyrighted the moment it was written, but I guess it would only be considered copyright infringement and not theft.

No, the law states "goods or wares", the code is neither.