I think I am using
http://www.ext2fsd.com/ for reading and writing ext2/3... I am not sure, since I am not at my PC now.
No, eliminating KoboRoot.tgz. is not the solution. You need to replace rcS by the original file.
If you do not have too many unsaved annotations, a factory reset might be the easiest way.
Edit: you can also extract the kbmenu folder from my KoboRoot.tgz file and copy it to .kobo. Then select install update from the menu (provided you have still the original KoboRoot.tgz on the reader).
Edit 2: If it is about the annotations: Since you have reading access to the SD, you could just copy the KoboReader.sqlite, and then make a factory reset.