If you point eac3to at the DVD directory root it should be able to rip the subs by episode. See the wiki for full info.
E.g, the below will extract (for title 3) the:
- chapters (track 2)
- video (track 3)
- audio (track 4)
- subs (track 5)
eac3to "G:\Galapagos HD DVD 1080p VC-1 DD 2.0" 3) 2: galapagos.ep2.chapters.txt 3: galapagos.ep2.mkv 4: galapagos.ep2.ac3 5: galapagos.ep2.sup
You will need to do this for each title and you can then use suprip to OCR the .sup file to .srt
EDIT
Alternatively, for .srt you could re-author the DVD using something like DVD Shrink which would allow you to split by episode. Your standard subrip would then read the new structure fine.