Although it's not entirely automated, there is a batch file that uses rtmpExplorer to download the flv, extracts the video url from the command.bat file it generates and feeds that into the subtitle downloader python script, uses an flv splitter to extract the 264 and aac, then mkvmerge on the video, audio, and subtitles to create a finished mkv file.
Basically takes several free scripts/apps and ties them together with a batch file. Not the most advanced thing in the world, but gets the job done on a Windows PC.
Code:
http://www.darkztar.com/forum/showthread.php?219034-Ripping-videos-amp-subtitles-from-Crunchyroll-(noob-friendly)