This is a silly conspiracy. The facts about the initial funding of research on Tor have always been public and well-known, and the conspiracy is based on the idea that there was some grand scheme looking forward into the future for more than 16 years. It's much more likely that some researchers at some government agency implemented the known idea of onion routing in a proof of concept, their work was more successful than anticipated, and later some other researchers at some other government agency were told to try to de-anonymize their colleagues' invention again.
However, I'd be more weary about more recent projects. A lot has happened during the past two decades in cryptography and privacy, and I do think it's credible that all kinds of agencies from all over the world nowadays have the task of subverting privacy projects right from the start. But back in the 90s? Unlikely.
Yeah, just because something was either invented or first implemented in the military doesn't mean it's tainted forever. SQLite was originally designed to be used on ballistic missiles. Heck, the internet itself was first developed by the DoD (ARPA). A lot of technologies have military origins.
However, I'd be more weary about more recent projects. A lot has happened during the past two decades in cryptography and privacy, and I do think it's credible that all kinds of agencies from all over the world nowadays have the task of subverting privacy projects right from the start. But back in the 90s? Unlikely.