Here is a way to delete a series of markers (I've been able to do this in version 2.0c, build 125 of VideoFactory)
Select a time region by clicking on an open area and dragging to the right or left, selecting a time range that includes multiple markers. Now right-click on one of the markers in that region. You should now see a choice that allows you to "Delete all in region" (or words to that effect).
If you've selected the entire time range of the project, all your markers will be gone... or, of course, you can pick and choose which groups of markers to delete.