For continuity's sake, you won't get any objection from me on the idea of inserting Freeman into that
3-second shot in the prologue of Fellowship. It's not really taking a huge chunk of Holm's part of the film out. However, seeing as it is a big moment for Bilbo as a character, some would probably object to it on the grounds that Ian Holm should be allowed to have that moment on screen in Fellowship since he did originate the role and is himself a Tolkien fan. That's more of an ethical objection to the idea though than anything else.
This actually brings up a good discussion point which I don't think has been brought up a lot in these threads, how would everyone feel if Jackson
did eventually decide to go all George Lucas on us and re-release the LotR trilogy in 10/15 years with updated CGI?
Bare in mind that part of the reason Star Wars fans hated all the changes Lucas made to the original trilogy were because he's also made the original, theatrically-released cuts of the films
impossible to find. What if Jackson/WB were to still alllow people to buy the movies in their original, 2001-2003 form? Maybe they'd be on a separate disc or something.
Personally I'd totally be up for that. Who would really honestly throw a fit if the Wargs got a visual overhaul to match their (apparently) better look in The Hobbit? Lord knows their effects have not held up well over time. Besides, there's no novelty factor for me in badly-aged CGI. With Star Wars, many long-time fans felt the movies lost a lot of their charm once Lucas started tossing in anachronistic CGI into every scene, whereas LotR made its name on it's digital effects.
Heck, they've already made slight alterations to the original cuts of the trilogy on the blu-ray releases, like the noticeable color-enhancements to the Council of Elrond scene. In the original film looked like it had been run through a pot of urine, whereas the BR version features a much better color palette and the scene doesn't look over-lit and muddy, it looks fantastic.