This is part of a wider Hardy theme of romanticising the old-fashioned ruralness of the SW England countryside and disdaining the march of modernity.
Such commentary appears a lot in Hardy's writing. In fact, the very idea of his Wessex is predicated on his desire to romanticise rural life in southwest England. As mentioned in this answer, he was trying to create a sort of 'Greek mythology' based in a land more familiar to him than Greece.
Some of his characters (such as Tess Durbeyfield/d'Urberville) are almost caricaturised in their ruralness, and they and their surroundings and way of life are contrasted heavily with modernity in all its forms. Here's another example (referencing the train to which Tess and Angel take the milk cans from the farm to be transported to London):
Modern life stretched out its steam feeler to this point three or four times a day, touched the native existences, and quickly withdrew its feeler again as if what it touched had been uncongenial.
-- Tess of the d'Urbervilles
The point of the passage you quote is to contrast "the original church", with its quaintness so typical of the English countryside, with the new "modern Gothic" building, described in much less romantic terms. It's a gentle putdown to the spread of modern ways and architecture in the rural regions that Hardy loved so much. Note that:
The old church is connected directly to the everyday lives of ordinary people living nearby, its stones used in their homes and gardens and pigsties. This emphasises how well it fitted into the local community.
The new church is described as "unfamiliar to English eyes". It's so outlandish to have modern architecture in this rural English village that it literally seems foreign.
The old church is described as "hump-backed, wood-turreted, and quaintly hipped". This may sound like a criticism, but do take into account how quaintness is often one of the defining characteristics of Englishness. (No source for this except personal experience - I've lived in England for most of my life.) It's traditional, its odd structure familiar and beloved to the locals.
Contrast this with the simple, unadorned words used to describe the new church: "a tall new building", "erected on a new piece of ground". There's no hint of beauty or romanticism here. It's not even described as a church, just a "building"!
The person who orchestrated the replacement is described in disdainful terms as an "obliterator of historic records". A person we don't care for, whose exact identity is far less important than their symbolic status as a representative of the spread of unseemly speed and modernity in rural England.
Finally, this person (George Edmund Street, most likely) hadn't even cared to stay in the village for longer than a day. The new church must have taken longer than that to build, but Hardy makes it sound as though it was a duff job knocked up in a day, as opposed to the old building with its centuries of history. Clearly, it wasn't a labour of love.
(The first half of this answer is partly inspired by discussion in Thomas Hardy and Empire: The Representation of Imperial Themes in the Work of Thomas Hardy by Jane L. Bownas and Catholicism, Sexual Deviance, and Victorian Gothic Culture by Patrick R. O'Malley. The second half is based on my own close reading.)