I've given this some thought (and I hope my belated entry here is not to late to shape your project).
Rather than come up with a complete and stand-alone solution, it might be better to simply provide additions to existing tools to help them support modern eBook formats. My specific recommendation is to provide a set of tools to be used in conjunction with LaTeX (pronounced "Lay-tech")
http://www.latex-project.org
that would support the Sony BBeB (.lrf) format, the MobiPocket format, and perhaps a few others.
If you wish to provide a GUI component using Qt
http://trolltech.com/products/qt
the provide a basic editor for the LaTeX work and then provide a "preview" function that would render the output in the format of the specific eBook reader targeted.
This approach has several advantages from a pedagogical point-of-view: we have now divided the problem into several distinct pieces:
1. LaTeX processing (no GUI component at all)
2. BBeB backend
3. MobiPocket backend
4. Editor
5. Previewer for BBeB
6. Previewer for MobiPocket
Additionally, students will need to work within an existing code base to extend it--something that is more "real-world" than the "start from scratch every time" approach most student projects use.
If the project is structured properly, new eBook formats could be added by subsequent projects. Further, using the comment LaTeX format means a single book source file can produce multiple formats with little compromise.
While WYSIWYG may be all the rage, WYSIWYM (what you see is what you meant) is actually more useful for this type of work.
I wish you and your students well. If there is anything else I can contribute, let me know.
-- Scott