Hi Dru,
Glad to hear you're loving qRules! :)
Do you have an ID field mapped to the ID column in your SharePoint list? I'd assume you do since you mentioned that editing existing questions work. So with the ID already in place, doesn't deleting rows from the form delete the corresponding items in your list already?
Marking items as Inactive is also a good way to go. For this, you just need to add an Inactive column in your list and in your form, and then map it. As long as the form stores the list ID and qRules knows that it is indeed the ID (by either checking the ID box in the mapping tool under Options or by adding /id parameter in your command), it should be able to update the corresponding list items.
Best of luck! And let us know if you get stuck - we'd be more than happy to help. :)