If the shock is bottoming out then there is no movement in the shock anymore. This means that it is basically a solid rod transfering all the energy straight through. If it doesn't damage the shock it will eventually break your shock tower or crack your frame.
Lower your bump stops a little.
I was afraid of that but I think it will be the only thing to cure the problem. I am running All Pro buggy leafs, once I re mount the bumpstops I will have 2" or less of uptravel before the springs negative arch. They are brand new and sit flat, so they will probably sag so they sit on the bumpstop all the time. I think my truck is too heavy for them.