Hello and welcome to BYC
First of all, worm eggs are often distributed by wild birds and even earth worms. They get around and no matter how well you take care of your flock, they can still get it. Pebbles has nothing to do with worms. Pebbles are used by chickens as grit to help them break up food in the gizzard. And talking of which, I would suggest you put sand on the floor of your run/coop. It will help keep it dry, the chickens will eat some of it (grit) and it's easier to clean and more manageable.
You will have to get a decent dewormer for your flock and I'm afraid the withdrawal period for most of them is 14 days, during which you should not eat, sell or incubate the eggs. Some recommended dewormers are Wazine, Valbazen or Safeguard. I've heard of using DE and other natural products, but I also heard they don't work very well. ACV is good for chickens though, so give them some every other week anyway, but like I said with an obvious infestation of worms the chemical route is the way to go. Good luck!