As you say, legal torrents exist (indeed, many open source projects rely on torrents because they can't afford the bandwidth costs of direct download). Therefore, a torrent tracker has both legitimate and illegitimate uses. Similarly, I can find legal and illegal content via a Google search.

There isn't any ambiguity here. Torrents and web search are both multi-use technologies. In the case of multi-use technologies, we should prosecute the criminals based on their use of the technology in question.