Using DQL, the below statement will be:
$query = Doctrine_Query::create()
->distinct(true)
->from("Users u")
->innerJoin("u.Workplaces w on u.workplaceId = w.id)
->innerJoin("u.Municipalities m on u.workplaceId = m.id)
->innerJoin("m.Prefectures p on m.workplaceId = p.id)
->innerJoin("p.Regions r on p.workplaceId = r.id)
->Where("w.shortName = 'ES' and m.id in ($esMunicipalityIdArray))
->orWhere("w.shortName = 'JHS' and m.id in ($jhsMunicipalityIdArray))
->orWhere("w.shortName = 'ES' and p.id in ($esPrefectureIdArray))
->orWhere("w.shortName = 'JHS' and p.id in ($jhsPrefectureIdArray))
->orWhere("w.shortName = 'ES' and r.id in ($esRegionIdArray))
->orWhere("w.shortName = 'JHS' and r.id in ($jhsRegionIdArray));