When diplomats get punished for doing their jobs

Agreed, this is a terrible article. It does not articulate the stated main point, which is what diplomats do that might be considered espionage.

Reading between the lines, the implication is that she passed information to Pakistan when 'official' channels of communication were closed. This was likely of critical diplomatic import to ensure that communication between the countries did not completely shut down, but was not officially sanctioned by either government.

If she is truly innocent, the real villains here are her superiors. She was ordered to provide a back-channel for information and when this was noted by another service, no one was willing to vouch for this. Almost certainly this was due to her superior's CYA. She was assigned something that was considered useful but not worth the possible political backlash if it came to light.

Alternatively, I do not understand is why she would not publicly state this. If she was ordered to do something, she should give names and dates of meetings when this occurred. The FBI would be obligated to investigate.

Meeting with officials of a hostile government in unofficial settings is the general shape of espionage.