To ignore duplicate keys during ‘copy from’ in postgresql

Use the same approach as you described, but DELETE (or group, or modify …) duplicate PK in the temp table before loading to the main table.

Something like:

CREATE TEMP TABLE tmp_table 
ON COMMIT DROP
AS
SELECT * 
FROM main_table
WITH NO DATA;

COPY tmp_table FROM 'full/file/name/here';

INSERT INTO main_table
SELECT DISTINCT ON (PK_field) *
FROM tmp_table
ORDER BY (some_fields)

Details: CREATE TABLE AS, COPY, DISTINCT ON