Okay... wait...
You're saying that if those guards outside of that one city in FFIX were important to the story?
What if they had removed them? Would you walk up to the city and go, "Well damn, there should be guards here or something. This game is clearly incomplete." I mean, when I see guards, I usually think "Oh hey, guards." I don't stop and contemplate the beauty of a rose. I don't wonder how the story of Abraham and Isaac somehow parallels Zidane's relationship with Kuja.
But let's take a step back for a second. What about the environs of another, hypothetical village.Two women are standing next to a well, and when you speak to one, she says, "It sure is hot today!" One could, I suppose, interpret this as being an important indicator of the weather. After all, a hot day could contribute to certain behaviors relevant to the story and the player's interaction with the world. But... What if every character in the village remarks about the weather in some way? What if the weather is already or repeatedly soundly established. This delegates this woman next to the well pretty soundly into the entirely inconsequential column on the galactic sorting chart of NPCs. Are you proposing that we stop to consider this woman's marriage, and take a moment aside to think about what a wonderful wife she must be to be fetching water, clearly for her husband? Maybe we are to conclude that women in this story really like water. That's important!
What if we removed one of these women? Would anyone but the creator know, or care? Would we be suddenly jarred to the unexpected realization that women like water in your RPG universe, far too late for the story to be saved?
But maybe you really mean the more important NPCs. Consider a character from Canadian Knights, Judge Pudge. Is judge Pudge important? Yes. Would you even notice if I flat-out removed Judge Pudge from the game? No. No you wouldn't. I could easily replace Judge Pudge with his daughter, Gillian, and you would never even know (if you hadn't read this post, that is). Oh sure, the scenes would play out differently and the jokes would need to be altered a bit, but we are talking about a small place between two stout brackets denoting a comparitively unimportant period of time in this universe. Everything outside those brackets remains entirely unchanged. Many RPGs are built from replaceable/moveable units like this. Not every unit can be removed, but many can.
Not every NPC changes the world, as you suggest. Remember, the only impact a NPC has on the world is the impact the writer gives them, except for a few exceptions. That statue bust you can examine in the halls of the castle, the nun with second thoughts, hell, even the reoccuring Trish the Heckler, Canadian Knight's very own O'Aka (spelling?), are ultimately only as important as their role in the story. If we removed Trish, the shopping dynamic would be changed, and a lot of good comedy would hit the cutting room floor, but this could, in fact, be an improvement.
I'm a writer of non-stop rhetoric. I talk a lot in life and I type a lot online. Recently, I wrote a research paper on ADHD. It had a strict maximum word count of 3000 words, and mine was 3900+. I had to make some tough cuts, but in the process of losing a lot of points even I felt were very important, the end result was much more efficient and concise.
There is such a thing as baggage. I've been trying to write a book for almost 8 years now, and while characters have come and gone, little else has changed thematically. The setting is still the same, and many characters go on as though nothing has changed. Is it bad writing that the outright removal of a major character leaves but a ripple in the overall work? No, I don't think so. Now, if I removed the hero, things would change. That mechanic guy? Yeah, I like him, and he had a lot of use in developing other characters, but in the end there are different ways of doing things.
Hell, I removed some of these characters based on feedback from friends. "I don't like the anthropomorphic rabbit character with no arms who uses his ears like fists!" Well, I thought about this. I thought about the arguements. I realized that the story could go on without him, and would probably benefit from it, so there he went.
Is this story incomplete? Yes. But that has nothing to do with the removal of a giant rabbit.
Your opinion or theory or whatever here flies in the face of the concept of revision, and critique. "Sorry man, I don't like all the furries in your game." "RACIST!" No, that doesn't fly.
Some character just plain suck and need to go to make the story BETTER. Some characters, even major character, need to be removed - need to be critisized - for a story to be complete.