It seems it's usefull to keep the migrate tables while you are working on migration, in case you need to see the mapping and revert/redoing stuff.
But actually I was having some troubling while using the migrate module for other pursings. This SQL error: SQLSTATE[HY000] [2002] No such file or directory
did keeping show up when I did try to use drush migrate:... till delete those tables.
With this query you can delete all table with prefix migrate
SET GROUP_CONCAT_MAX_LEN=10000;
SET @tbls = (SELECT GROUP_CONCAT(TABLE_NAME)
FROM information_schema.TABLES
WHERE TABLE_SCHEMA = 'db'
AND TABLE_NAME LIKE 'migrate\%');
SET @delStmt = CONCAT('DROP TABLE ', @tbls);
-- SELECT @delStmt;
PREPARE stmt FROM @delStmt;
EXECUTE stmt;
DEALLOCATE PREPARE stmt;