Your poor ancestor obviously encountered a rather censorious vicar! In most such cases, the father's name is left blank (or diplomatically declared to be deceased with or without a fictitious name).
What people scribble down on census forms and what they look a minister of religion in the eye and tell him can be two very different things. So the man who put your chap down as his son in 1861 (easier than writing "wife's son") may or may not have been his real father, but one can probably assume that he wasn't married to his mother. Presumably you have not found a birth certificate or a marriage of those purporting to be his parents in 1861?