The user export currently exports with deleted/inactive users as red type with a strike through.
This is visually a nice way to easily 'see' who is and is not active, but does not lend itself at all to any automated ETL of the data.
Adding a column to display active status would make processing the data in the file much simpler. And since filtering data on a column such as 'active' as a boolean is very simple the option to include inactive users or not could be removed from the process.