I'm not sure if this would help the situation or not, but Pismo Mount could possibly help here:
http://www.pismotechnic.com/pfm/ap/This allows you to mount an ISO where it is in your folder structure. So as an example, if you have a folder named "Blurays" that contained a bunch of ISO files (Avatar.iso, Spiderman.iso, TheAvengers.iso, etc.), you could mount all of the ISO files and end up with a folder structure that looks like:
..\Blurays\Avatar.iso\BDMV\...
..\Blurays\Spiderman.iso\BDMV\...
..\Blurays\TheAvengers.iso\BDMV\...
At this point, JR Media Center would have no idea that these are iso files - it would just see them as a bunch of BDMV directory structures. You could even drop the iso extension from the filename to make the directory structure look cleaner when the files have been mounted (Pismo forces the mount name to be the original filename). So if the iso files had no extension, the directory structure would look like the following after mounting:
..\Blurays\Avatar\BDMV\...
..\Blurays\Spiderman\BDMV\...
..\Blurays\TheAvengers\BDMV\...
There's a command line interface for Pismo, so it would be possible to setup a script to mount all the iso files when the PC boots (the mounts don't survive reboots). This would also give one a way to automatically mount newly ripped movies.
AFAIK, there's no limit to the number of iso's that Pismo will allow you to have simultaneously mounted unlike most other mounting tools, such as Virtual Clone Drive, that are limited to some number of drive letters so it should be possible to have a sizable Bluray collection mounted all at once.