You can already work with Non Primary Unique key. The only reason I can think of for the issue you were having is you had Skip option selected for the columns selected in Primary key in Profile settings.
When I change my import profile operation from "insert" to "update" I get a "Select Primary/Unique Key" message. I can't get past this no matter what fields I select, and I have verified and re-created unique keys on the tables. What am I doing wrong?