The Halos were safe havens, for the most part. It was convenient for indexed species to be kept on the Halos because they were the most protected, the Halos were no danger until they were actually fired. They weren't just biological preserves, they were mobile and well-fortified nature preserves. Before the Halos fired, the indexed species could be relocated to the Ark. It wasn't until the Master Builder decided to start using the preserved specimens for experimentation on the Flood that the Halos, like Installation 07, became something more like torture grounds.