She is listed as Roman Catholic in the 1901 census (James isn't in the census, having died in 1883).
That being said, there are also non-catholic Lamonts in the area, so I can't discount her being the convert either.
I still think it's most likely that James was the non-catholic. Looking at where Eliza is living as of the 1901 census, she is living in Drumads, Tyrone on land rented by Arthur Hamilton Bell, a Presbyterian. He is living a few houses away with his brother, a David Miller Bell, and a deaf and dumb sister, Annie Johnston (she's unmarried, so I've yet to figure out the different surname). They have a catholic farm servant James Bell, 14 - just a bit too old to be one of James and Eliza's children.
Eliza's son Hugh, my great-grandfather, is living in nearby Aughaveagh on land rented by the 'Hamiltons of Drumads'. As Arthur's middle name suggests, the Hamiltons were related to this other Bell family through marriage (Arthur and David's father was Hamilton Bell, son of a David Bell Esq and an Eliza Catherine Hamilton).
By 1911, Hugh and family have moved to Drumconvis, neighbouring Drumads. They are living on land rented by an Agnes Witherow Bell - the widow of David Miller Bell. It's all circumstantial, of course, but I suspect there may be a family link here, however distant.