The linked article is a rather uncritical piece on Robert Harris's restoration effort on Godfather I & II. If there is such a thing as a celebrity in this field, it is Harris, who has worked on a number of very high-profile restorations (eg. Vertigo, Lawrence of Arabia). Unfortunately, these projects were driven by commercial as well as preservationist motives, and as a result suffered some anachronistic alterations and compromises.
The International Federation of Film Archives has a Code of Ethics that lays out commonsense guidelines for respecting the integrity of works being preserved:
1.4. When copying material for preservation purposes, archives dowill (sic) not edit or distort the nature of the work being copied. Within the technical possibilities available, new preservation copies shall be an accurate replica of the source material. The processes involved in generating the copies, and the technical and aesthetic choices which have been taken, will be faithfully and fully documented.1.5. When restoring material, archives will endeavour only to complete what is incomplete and to remove the accretions of time, wear and misinformation. They will not seek to change or distort the nature of the original material or the intentions of its creators.
Portions of Lawrence's dialogue and much of Vertigo's soundtrack were re-recorded from scratch (i.e. not from existing elements) and in stereo, which Vertigo never had been. Now, the Godfather films have been scanned and manipulated in the digital domain. From the article: "Harris determined that a photochemical restoration was out of the question. 'Not only that,' he says, 'but we determined that the original negative of The Godfather should never be run through a pin-registered mechanism. It could crack up.'" What he really means is that the results wouldn't satisfy today's audiences who are used to watching sanitized DVDs, that the elimination of artifacts of the process of production or subsequent damage trumps getting a real sense of what the work truly is. The result is a mis-education of the casual viewer and a gnawing sense among the well-versed that something is amiss. We have lost the delicate play of light, the lushness of color, the integrity of the image.
It might well be out of the question to make scratches and tears disappear entirely and seamlessly by photochemical means; restoration is never a perfect process. But repairing actual elements minimizes generational loss without altering the basic character of the imagery (as would scanning). Cleaning and wet-gate printing uncover actual photographic imagery, whereas digital dirt and scratch removal can only interpolate missing data. For true preservationists, manually patching up film elements, culling bits and pieces from various sources, cleaning them, and wet-gate printing them are routine (though arduous!) tasks. Robert Harris is very familiar with this type of work.
If the ethics of preservation truly were a priority, every effort would be made to utilize authentic elements, and reconstructed elements would not be snuck surreptitiously into the end result. But too often we see a contrary ethic in action, disastrously: the entirety of the work is altered so that any transition between the genuine and the reconstructed may be made seamless.
Digital intermediates are common in film production today, and that's a big reason most films don't really look (or act) like films anymore. They don't have that purity of image, that snap to them that says "I am an imprint of reality". Now the Godfather films have suffered this same fate; at the visual level, they have been removed from the time in which they were made, they have been aesthetically decontextualized.
(Spoiler warning!)
When Don Corleone's funeral motorcade drives through the cemetery towards the end of The Godfather, the backdrop of sepulcher-dotted hills looks like it could have been mocked up on a computer. Surely this is not one of the tragic overtones this scene is meant to carry.