Absolutely not. The government is not one unitary piece. The NSA is not the ATF is not the FBI. These capabilities were likely kept secret from other government

Absolutely not. The government is not one unitary piece. The NSA is not the ATF is not the FBI. These capabilities were likely kept secret from other governmental agencies as much as the public. Furthermore intelligence agencies are well aware that every action communicates information back to their adversaries. It's a no-brainer to let Silk Road exist if you think doing so gives you the edge on terrorism, or otherwise furthers the national interest.