Free speech really should not be able to qualify as treason, although there are some who interpret the text less strictly might consider some speech to be giving enemies aid and comfort.
I think that premise (That speech can be giving enemies' "Aid and comfort") to be pretty absurd. Even saying "Go Osama Bin Laden" wouldn't really apply because its not really aiding him in any tangible way (Yes, I know he's dead, dead guys make better examples

)
Generally that would be termed Sedition rather than treason though. The first amendment most certainly should invalidate legislation like the Alien and Sedition Acts.
I've always thought this was so obvious I didn't get how someone living so close to the bill of rights passing could have gotten it wrong. The reality, as you say, is probably that he didn't care. Kudos to Jefferson and Madison for fighting against it.
Federalists like John Adams showed great disdain for the bill of rights (which of course had been pushed primarily by their political rivals, the Anti-Federalists, who had a very different view of the role of government) in supporting such legislation. They went so far as imprisoning people (including congressmen) and forcing them to pay fines worth over $70,000 in today money just for criticizing the president. This is a case where judicial review probably should have been used to overturn the statute, but the supreme court never heard the cases. (Instead judicial review was established after the Federalist court packing, in a case where Marshall's ruling made no sense in the light of the clauses immediately before and after those on which he focused.)
Unfortunately the early governments existed in a time of kings and dictators, and the United States government was really the first of its kind, even though the President and Senate weren't democratically elected. The Founding Fathers had a vision for how it could work, but then found it inconvenient when they took power. I'd insist, in spite of the arguable compromise with the Louisiana Purchase, that Jefferson was the lone, glaring exception. And in his case, it was actually a COMPROMISE, with debatable constitutional legality. I think I would consider buying land to be a treaty, at least of sorts, although I do agree a clearer amendment would have been better. The Alien and Sedition Acts, on the other hand, aren't even debatable, nor is the modern Patriot Act.
I think they really could have gotten better, but John Marshall screwed us over way too much. Sometimes I really do wish the South won....
The acts were extremely unpopular and were the main reason why the Federalists lost control of the government (except the Judicial branch, which they packed with as many of their cronies as possible) in 1800. The Democratic-Republicans didn't actually overturn the laws either though, they just let them expire after pardoning those who had been convicted under the Federalists and then using them against their own political rivals for a time.
When did Jefferson and Madison actually use those laws? Admittedly that's not something I've ever heard before.
I hadn't really thought of it like this before, but it really does seem like freedom of the press ought to overrule the authority of congress to grant the legal monopoly of copyright protections. Copyrights did originate explicitly as a tool of censorship. (Plus, of course, there is good reason to believe that in their current form they hinder the progress of science and useful arts far more than they promote them.)
Since the first amendment comes later, it would trump any article that contradicts it, I agree. That said, how exactly does copyright work? I don't see freedom of the press as giving a right to steal stuff from other people, although that would depend on how its applied. If I write and publish a book, I don't want someone else selling it and taking the money.