it wasn't "an exploit" for someone to make an item to npc then either. they did call it one and said it as their reason they dropped the amount back then as well. all they should do is make either the price given by the npc dramatically lower or the amount the npc's will buy the drops after. they need to put it inline with the rest of the economy.
remember they call it an exploit anytime you are doing something they didn't intend. they called having high enough dps to kill garuda before astral flow an exploit. they called making too much gil making and selling items to the npc an exploit. using that line of reasoning they have used up to this point would make atomos spamming an exploit as well.
personally they either need to reduce the amount of seals per 4 crystals down to like 250 per 4 or reduce the amount the npc pays for the drops after. along with one of those they need to make it to where you can only check the stone once.
they dont have to completely gimp stop the selling, but they need to make atomos more in line with the rest of ways people are able to get seals.