Just so I'm being clear, Silverlight is used for viewing Photosynths, not making them.
Making them will definitely require running Windows - whether it's a native installation or virtualized. If you're going to run a virtual machine to make your own synths, then you may as well use the viewer on the same VM.
Even though this workaround exists, ideally the Photosynth team will see fit to simply serve the Silverlight 2 viewer to Linux users until Moonlight 3 is finished, as we suggest. I think for usability reasons, the Silverlight 2 viewer+editor should be served by default to Linux users, with a link underneath each synth to test the Silverlight 3 viewer.
This needs to be addressed because Moonlight 3's final release is scheduled for September 2010, whereas Silverlight 4 is scheduled for a July 2010 launch, continuing the lag game.