My problem with the Turaga system is the ease with which the powers can be abused. There's nothing that prevents them from committing atrocities on the Matoran. Clearly, this never happened, nor would the former Toa Metru ever do such a thing, but there is no real "check" that I can see that prevents this sort of thing from happening. If the Piraka had been smaller in stature, it would have made sense for them to pose as Turaga and spread their ills in that way.
As to the Toa exterminating a species, I am referring to the Avohkah, the sentient light creatures in Karda Nui that the OoMN tasked the Toa with eliminating. The Toa did so, simply following the orders of the OoMN, a far cry from Lewa Nuva stopping Jaller from killing an ash-bear. Real world examples include the hunt of the mammoth, the hunt of the buffalo, and a certain type of small bird (can't remember the name of it, sorry), which is why I included it as being dark.