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"intellectual property"

That's a really muddy term. How exactly can you protect a protocol? Trade secret? Patents?

Copyright shouldn't apply if it's a reimplementation.

Edit: s/since/if/

While copyright wouldn't apply to an independent reimplementation, the article included links to decompiled versions of the Skype binaries, which would definitely fall under Skype's copyrights. Nothing wrong with using those decompiled binaries to reverse-engineer and document the Skype protocol, and I hope this produces useful results there, but that doesn't make it OK to directly redistribute the decompiled binaries.

The easiest way to is to restrict the right to reverse-engineer in the Terms of Service of the Skype client (which he needs to use, in order to have something to reverse engineer.)

Terms of Service don't necessarily have any legal force, and many jurisdictions have legal protections for the right to reverse-engineer, particularly for interoperability purposes.

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