It's not the leaking of trade secrets that's criminal, its the theft of the associated intellectual property. If you assume (as US law does) that intellectual property has a value and its theft is equivalent to theft of physical property, then it makes sense that it's a criminal offense in the same way as a physical theft (and probably also a civil matter).
Not all intellectual property is legally protected against theft this way though (otherwise any disclosure of IP could be theft). The bar for intellectual property to be legally considered a trade secret is high. If the IP isn't sufficiently secret, it's legally less clear whether you can really steal it. Just stamping it "secret" isn't enough. To be a trade secret the company needs to prove that it's a secret, that the secrecy of the IP is highly valuable (for instance loss of the IP's secrecy hurts a competitive advantage), and that they've made significant attempts to keep it secret by limiting access to "need-to-know" people and protecting the IP though appropriate security and secrecy.
In this case, it sounds like the defendant may have gained physical access to a building he didn't legally have access to (ie company made an attempt to limit access with some security) and copied data off a server. MS is arguing that this hurt them financially.
A defense against this might be to claim that even if the data might have been valuable and releasing it harmed the company, they didn't treat it with enough secrecy/security for it to be considered a trade secret. If that's what the court decides, then there could still be a civil suit (breaking employment NDA contract, etc), but it wouldn't be a criminal matter.