Let's say we, as a nation, through our elected representatives, decide to pass a law against trojans. Then let's say there's a site hosting a trojan repo, open to the public, and they refuse law enforcement's demands to remove access to the code. So the FBI goes through the court and gets a warrant to seize the site and prevents access to the code.

Would you stop the above chain of events at the very first link? Would you say: "We can't ban trojans because it's code, and code is speech, and speech is either free or its not?"