I still haven't had my hands on any HDV, but I wonder if you might somehow export just the speed effected clips as self contained movies, then re-insert them in the DV timeline?
So - make a new timeline, drop in your (real time) clip, export as dv, reimport, then apply speed changes on the DV export timeline.
Someone else probably has a much simpler and more elegant workaround, but this came to mind as a breaking point solution.