As a professional historian, I'd say that as long as Jackson is not passing it off as replacing the original film evidence, attempting to deceive, then there's little to worry about here. Strictly speaking, historians "manipulate" the evidence every time we do anything with it. Even a museum that merely puts it on display in its "raw" form is manipulating it in all sorts of ways: it places in a specific environment, with explanatory text (the display card) that inevitably pushes viewers to see the source in particular ways, and as a part of larger themed exhibit. This display context / environment is definitely a form of manipulation and alteration. Similarly, even a typeset version of a manuscript prepared for publishing is a form of manipulation as it standardizes and otherwise regularizes the source, eliminates mistakes and marginalia, etc., etc., not to speak of any historical writing that interprets the evidence. (For fun look up how much literary scholars argue and fight over the published versions of Joyce's Ulysses -- simply preparing the manuscript for publication is a fraught business that inevitably is full of manipulation and interpretation.) So, to my historian's mind, there's little danger of a project like this supplanting the real sources except in the mind of the ignorant and willfully uninformed. Any serious historian would be painfully aware of the technological limitations of the era she is writing about and thus would not be taken in. Historians habitually train a very critical gaze on their sources and the vast majority of us are not easily fooled. (Those that are tend to be corrected rather bluntly and publicly by our colleagues who read our work with what I sometimes call "aggressive skepticism". There's a genuine professional incentive to be careful as a gaffe can be disastrous for one's career, peer respect, publishing prospects, etc.)
As for bringing a time or experience "back to life", obviously no sane person would actually want to re-live WWI trenches. But grasping a closer approximation of what some parts of that experience was like would be a positive gain in most historians' eyes. Grasping and grappling with the dark parts of history, no matter how ugly and unpalatable, has educational and research value.
Caveat: I haven't read the linked articles -- too busy preparing for tomorrow's class. So, if Jackson is indeed trying to get archives to use his altered film in place of the real source footage then I'd only have to say that he's a fool. EDIT TO ADD: If his process actually destroys the original source footage, then I'm shocked and dismayed and he should be stopped.