The point is that the CIA would need many non-CIA individuals in the US using Tor to effectively mask CIA traffic. Sure, if SOPA outlaws Tor that would not prevent the CIA from using it, but if it effectively reduces the number of others using it, then Tor becomes useless for the intelligence community.
Edit: Also, thanks for the link. I had forgotten, but the Tor project tacitly admits to an ulterior motive from the intelligence community.
But I don't think the CIA would care about SOPA. They are quite able to use "illegal" technologies, and don't need the law changed to do it.
[1] https://www.torproject.org/about/torusers.html.en