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