In terms of content, the point of literature courses is to familiarize the students with the subjects, arguments, and contexts of the literature; in terms of skill-building, the point of literature courses is to teach students (new) methods of reading that facilitate understanding the literature. This typically means overcoming the students' belief that they know how to read. Using a new medium for their writing (hypertext) helps make clear that new methods for reading are necessary.
This is one case where transparency is a hindrance-- the process of creating hypertexts is sufficiently different from writing papers or essays that the students are forced to consider the way they read and write.
One thing to be careful of when using this technique, it seems to me, is that you re-associate the skills with reading when you're done. You don't want students thinking that the reading skills they are learning apply only to working with your software or with hypertext.