This isn't a permanent solution, but it's kind of a workaround. apt-file doesn't seem to allow the plus sign to be in the protocol name, I've changed it to change it to torhttp. After that, add the following line to your /etc/apt/apt-file.conf and it should work. Be careful, though, because torify isn't perfect, and I don't know if it preserves anonymity when used with diffindex-download.
torhttp = torify diffindex-download -i `echo <uri>/dists/<dist>/Contents-<arch>.gz | sed s/torhttp/http/` <cache>/<dest>
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