Your point about the preservation of discussion data after a course is closed is well made, and philosophically well aligned with our preference for learners to be in control of their own data. I agree that users who are not experienced in using a variety of technologies will have usability issues until they become more familiar with a range of tools.
The issue is that our design must take flexibility into account creating opportunities for a variety of different tools to be used which can be aggregated into the timeline. So if we augment by offering local discussion forums in the wiki - we must also provide a way for the threads and posts to be integrated into the WENotes timeline.
WikiEducator was an early adopter of LiquidThreads -- the threaded discussion extension used on our talk pages. Our version is outdated due to a nunmber of legacy dependencies and we are keen improve the discussion engine. Looking to the future, we will most likely implement Flow as the preferred wiki discussion tool. However, Flow is still under development and not quite ready for showtime and live course delivery. Take a look - Flow is impressive.
Flow is a very good and powerful widget. I went through their discussions and FAQ's and found that the server script to move LQT to Flow still needs to be developed.(or is it already developed?) This will pose a major issue of porting the old data if the script does not come up any time soon. Based upon the discussions that are present, there are many organization using LQT and are less keen on shifting to new widget. And even if they are to move to Flow, the script is a necessity.
You as well might have thought about this issue.Another naive solution will be to adopt Flow on testing basis for wikieducator. Users will use this and based upon their feedback, changes in Flow widget can be made accordingly(this is another project in itself). It will as well help the developers.