Most academic computer science is funded by the American government. Does that mean that all academic computer science is backdoored by the military?
To put it more specifically, most compilers researchers I know have at some point been on a DARPA grant, because DARPA has money and academics want money. I'm sure plenty of LLVM contributors have been paid from DARPA grants. Is LLVM backdoored?
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On an entirely different point, how is Freenet even comparable to Tor? They address totally different use cases (Tor is an anonymizing TCP overlay; Freenet is a distributed censorship-resistant store), and have very different threat models.
Further, it seems very unlikely that Tor (which is a piece of very well-maintained software with some of the foremost privacy researchers working on it) would have fewer bugs than Freenet, which is a sprawling Java program maintained by one man. Further, the security of Freenet in abstract hugely depends on having a functional small-world network, which requires Freenet to have been widely adopted to start with.
The comment parent's request was vague, but you simply cannot replace Tor with Freenet because they do totally different things. It is nonsensical to compare them because they address different threat models and accomplish different goals.