I bought my Russian tortoise named Spourd at Petco, and the conditions he and the other tortoises were kept in was totally acceptable. The substrate was clean, he had water and food, had popper heating, and his beak was trimmed. I have had him for 2 years, and he is 100% healthy. I think, if you see tortoises kept in bad conditions, don't buy it, because that is supporting the business. Overall, I think that buying tortoises from big chain brands is usually OK.
If you really check into PETA they kill more dogs and cats than anyone in the U.S. they would rather kill an animal than have it live in captivity. Be careful when watching their video's all is not what it seems.
Those pictures were mainly of small, post-hatchling size turtles, which have been illegal to sell in the US for years. I highly doubt those were being offered for sale at a Petsmart or Petco