But, it seems to be too slow (it is running from three days... ).So, before to kill the process, I like to know if some trick exists to make it faster.
So I've rewritten your original query as follows:
CREATE TABLE diffe AS
SELECT a.pk_uid AS uid_a, m.pk_uid AS uid_m,
ST_SymDifference(a.geometry, m.geometry) AS geometry
FROM poligons001 AS a, poligons002 AS m
WHERE ST_Intersects(a.geometry, m.geometry) = 1
AND m.ROWID IN (
SELECT ROWID FROM SpatialIndex
WHERE f_table_name = 'poligons002' AND
search_frame = a.geometry);