I think that the ideas that you've voiced are probably the general ways to do this. My reaction is that there are probably two different ways to address it, both of which are more-or-less equivalent, and both of which are really what you've already suggested.
The first is to reset due dates for a group of students, as you suggest. This is, however, easier than editing them one-by-one: I would start on the base Instructor Tools page, change the display setting to show only one section, select all students and the set I wanted to change the dates for, and then click "Edit set for user(s)." This allows you to change the dates for all selected users on that set. It does require that you change the dates for each set, but allows you to do it for all students you want.
The second is to have different sets for the two sections. Again, because the Instructor Tools page allows you to display only students in one section or another, you can select all of those students, the sets in question, and click 'assign' to assign the set. The only rub is that this requires that the sets for the different sections have different names, but that's probably a solvable issue.