The creation of the Deleters was something that the Alter organization saw as a must. It was something that everyone believed was needed to proceed with their goal. For one, to protect the world that they currently resided in, Pagna.
It wasn't their world, and they were visitors, so they wished to put away artifacts powerful enough to affect the world of Pagna. It was a just cause that allowed them to save many lives.
However, the organization would also know, there would be many that disagreed with that, and even in Alter, there would be those that might change sides, or decide that the goal they strived towards was no longer just.
Because of all of this, the Deleters had been created. They, at times, needed to stop powerful artifacts that had already gotten into the hands of those in Pagna. Perhaps powerful clans that had them.