You have misinterpreted the statement regarding St. Mary's on the Wexford parish website. When they say that St. Mary's was "the last Parochial Church in use from the time of the Reformation until the building of the new Churches in 1858," that does NOT mean that St. Mary's was in use until 1858. What they are referring to is that there was technically no parish church from the destruction of St. Mary's in 1649, until 1858, a period of over 200 years. A parish church is a church owned by the parish, and controlled by the Parish Priest. There was no such church from 1649 until 1858. Instead, during almost this entire period the Franciscan Friary was used, by courtesy.
I am unaware of any change in parish boundaries until recent times. Listings of townlands and parish maps are available in documents on the Wexford CC website. I think these are also listed in the pinned resources section for Wexford on this forum.
As for an increase in numbers of Kirwans, you must remember that there was a dramatic increase in the population of Ireland in the 100 years preceding the Great Famine. An increase of a factor of somewhere between 3 to 6. It is therefore to be expected that the population of Wexford also increased, and by extension, the number of Kirwans.