Silverlight is detected + functions in IE11 on other sites, such as Bing Maps' Map Apps ( http://bit.ly/photosynthcoverage ) and the Get Silverlight page ( http://microsoft.com/getsilverlight )
I know that the Virtual Earth plugin has been retired and it wasn't ever Photosynth's responsibility/jurisdiction, but I thought it bore mentioning as it might offer a clue.
I can still get the globe to load by going to http://atlas.freshlogicstudios.com/ and pressing the  key after clicking the map, but other keyboard commands no longer send as they did in IE10 on the same machines days before I installed IE11.
Other instances of the VE control (Bing Maps AJAX 6.3) fail to load completely ( http://virtualearth.natelawrence.net/ ) when they worked just prior to the upgrade.
I do realize that with IE11, you'll be moving to WebGL in both Bing Maps and Photosynth, but I'd still like the legacy viewers to function, as I trust they'll be kept for users who can't run IE11.