Transmission put up a new version - 2.92 that supposedly checks for and removes the malware.
So clone the last release version you trusted, build that from source and be happy?
The current version could be being compromised this minute for all we know.
Transmission was and remains my favorite torrent client on OS X, although I still like the torrent information presentation uTorrent had, and I still will run my old pre-adware 1.6.4 if I want more detail on a swarm.
Given that older versions still work, it seems exceptionally silly to delete an old version because of a site compromise.