Perhaps this will help you.
In LDS (taken from Civil registration) we have a Thomas Hunter born 1864 to Alexander Hunter and Isabella Irvine in Greyabbey.
Looking at the marriage of Alexander and Isabella in Ballywalter Presbyterian Church in 1845 (Emerald Ancestors)
Alexander's father was probably James and Isabella's father was probably John (AncestryIreland).
In Griffiths valuation(circa 1864) we have Alexander leasing a house and 10 acres of land in Whitechurch Townland in Ballywalter Parish, and two John Irvines leasing land in (1) Ballyboghilbo Townland and (2) Tullykevin Townland in Grayabbey Parish. These two parishes adjoin and the townlands are a couple of miles from Whitechurch, so it seems possible that you have found the right marriage.
It looks to me as if Thomas was the youngest child, born after registration.
So, perhaps Samuel was baptised in the same church were his parents married. If you look at Ros Davies site under churches you can find if there are records available to search for that church.
This information is all surmise, and the route I would follow, but worth a good look. RosemaryJoan