What the appellate court held was that just because source code may be used to instruct a computer does not mean that it's not speech when used "to convey ideas and to communicate." That does not mean that source code is speech when used to instruct a computer. It means that source code isn't not speech just because sometimes you use it to instruct a computer. Logically, those are two very different statements.
The court wasn't saying that the government can't regulate what you can and cannot program a computer to do. It was saying that the government cannot restrict sharing of source code between people, which is often used to communicate ideas.
The court wasn't saying that the government can't regulate what you can and cannot program a computer to do. It was saying that the government cannot restrict sharing of source code between people, which is often used to communicate ideas.