I think this is more of a general commentary on the state of the English countryside at the time, rather than a reference to any particular person.
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 and "unfamiliar to English eyes". It's a gentle putdown to the spread of modern ways and architecture in the rural regions that Hardy loved so much.
Similarly, the person who orchestrated the replacement of the ancient historical building 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. As for "certain", I think this word is used in the OED's sense A.II.7, probably a with perhaps a hint of e:
a. Used to define things which the mind definitely individualizes or particularizes from the general mass, but which may be left without further identification in description; thus often used to indicate that the speaker does not choose further to identify or specify them
[...]
e. Sometimes euphemistically: Which it is not polite or necessary further to define.
Calling the person "a certain obliterator of historic records" doesn't mean they're someone we should know about, or a person of interest in any sense. In fact, it's more the opposite: they're a particular individual, but not one whose identity needs specifying - perhaps even one about whom it is distasteful to speak further.
(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.)
