Not quite. That only applies if the government wrongfully acquired the documents, knew they were wrongfully obtained, and used them anyway. It is typically avoided by claiming they didn't realize they were wrongfully obtained and they were acting in good faith.
Wikimedia learned of the violations through legally available public documents.
The violations were more than just eavesdropping. The publicly available leaked documents claim the NSA falsified records and used the Wikipedia trademarks to help claim the validity of the pages. Even if part of the suit gets dropped, portions of it document clear civil violations.
While the government can do quite a lot to lie and convince others they are not the government, the Lanham Act is clear that the federal government is liable at the very least for their spying program disrupting the site and using their marks. Specifically in 15 USC 1114, it is against the law for "any person" to reproduce, counterfeit, copy, or imitate a registered mark when it is likely to cause confusion, or to cause mistake, or to deceive. Deception is exactly what the government did. The law continues: the term "any person" includes the United States, all agencies and instrumentalities thereof, and all individuals, firms, corporations, or other persons acting for the United States and with the authorization and consent of the United States, and any State, any instrumentality of a State, and any officer or employee of a State or instrumentality of a State acting in his or her official capacity. The United States, all agencies and instrumentalities thereof, and all individuals, firms, corporations, other persons acting for the United States and with the authorization and consent of the United States, and any State, and any such instrumentality, officer, or employee, shall be subject to the provisions of this chapter in the same manner and to the same extent as any nongovernmental entity.
That is quite clear, law twice declares that nobody in government is immune from that law. They stated it twice, just to be clear that it applies to everyone in government. :-)