More news: I managed to get the basics to work and built a simple demo application. All it does at the moment is controlling the LEDs, but I'm planning to add more options like disabling the wifi timeout or hiding annoying UI elements.
As before, the source is at https://github.com/ah-/koboplugins
and if you just want to try it, copy the attached library to /usr/local/Kobo. To activate it you have to open the library once, to deinstall it just delete libtweaks.so.