Alright, this is just speculation, but could Richard's freak out have been because of an unfulfilled promise that Jacob made to Richard kind of like the promise that Jacob made to Dogen about "making sure that his son will survive but Dogen would never be able to see him again".
I think we will see a scene where Jacob will free Richard from being a slave with the stipulation that he stays on the island and never returns to the Black Rock (Richard says this is the first time he has returned to the ship) and in exchange for Richard's loyalty and service to Jacob, all the prisoners on the BR would survive and also be free (however, like Dogen, Richard was told he would never be able to see the slaves on the ship again). The reason Richard was disenchanted by Jacob was because he saw the Black Rock and every prisoners dead bodies were on board.