I have a pencil type urchin from Florida, Eucidaris tribuloides. It has eaten algae for some time until, last month, it took a bite out of one of my gorgonians. I had to give it a shake to remove it, and the tissue was removed.
The longspine isn't suppose to resort to carnivory as often as the one I have (according to Shimek's book.) Are you certain that the urchin ate the zoa? If it was only a single polyp, perhaps the urchin simply dislodged it and it is still somewhere in the tank.