Hi, pomegranate is not toxic and can be given in moderate amounts. As long as he has not eaten the rind and not taken too much I don't think that has caused the GI upset. Unlink small dogs It should not be very difficult for a golden retriever to pass the seeds out, but next time you can give him fresh pomegranate extract or juice (home made, commercial juice will have lot of sugar) instead. You can start him on a probiotic, synfosium is a good option one a day for a week.
However if he is not feeling better please get him checked and see if we need to start him on some antibiotics. You can keep him on boiled eggs or boiled chicken breast muscles (shredded), white boiled mashed potatoes and white rice(overcooked and soft) for now, this would be easy to digest. Also avoid giving and other vegetables/ fruits for now.