I think that's just their easy way to emphasize Konoha is the righteous village of the highest morale and best people. Whilst there have been villains from Konoha, like Orochimaru and Itachi, most of the baddies have been from elsewhere, and apparently belonged to the normal class of ninjas actually (or ironically) doing what they had been hired to do (and some of them of course became "better" human beings after encountering Konoha ninjas).