So, using your code above, I ran
./join.pl --delimiter , --on 1 --missing 1 --missing 2 --warn-on-dupli
+cates 1 --warn-on-duplicates 2 --progress usa_ldap.csv HPSMcmdb.csv
In the case where the key was missing in file 1, there is no key output for the line.
I guess what would work for my data is if the key from the right file were output in the left key column (which for me is column 1).
I am looking into the code to figure out how to code that specific special case - but if anyone already has a solution, I would really appreciate it.