Hi, The staff at Kadamba bus stand once told me that there was a direct bus from Margao Kadamba bus stand to Gokarna around 2 pm each day. We have never gone for this option as it is too late in the day for us so we usually get a bus from Margao Kadamba to Karwar, another from Karwar to Ankola and finally a bus from Ankola to Gokarna. We have never had to wait very long for connections and prefer to travel this way rather than wait for the train which is always late!
Good Luck!!!