I think the "warforged ninja" thing is also a question of rules introduction as well though, or how much add-on rules does a GM want to deal with. A better example would be a Psionic character. Is a GM who doesn't want add-ons like Psionics handbook or Complete X a bad GM because he's stifling his characters creativity? I think one thing alot of players don't realize in this situation is that the GM is dealing with way more rules per session than a single player ever will.
Actually, I would personally likely be more accepting of a mechanical reason for not including something than a flavour one. Psionics is a perfect example. I regularly veto psionics because I have no interest in it and am too lazy to learn the rules.
In the case of my World's Largest Dungeon game, I vetoed the Vow of Poverty. Not because of the power issues but because the VoP sidesteps pretty much all the basic challenges of the WLD. Since there is next to no crafting in the WLD, pretty much everyone is under the same constraints as a VoP imposes. The realities of the campaign made the limitations of the VoP no longer limitations.
In the same way, I'd likely have problems with Warforged in the same campaign. Not needing to eat, being immune to disease and not needing to sleep sidesteps a fair chunk of the challenges for the first third of the campaign (around 1-7th level). In that setting, I'd probably whack on a LA+1 simply because the base abilities become SO powerful and desirable.
To me, there is a difference here though. If the objections are purely flavour based, such as Molonel's objections to my WF Ninja, then, it is the DM saying that the player's imagination isn't good enough. It becomes solely the DM's campaign and the players are passive users, rather than creators. Actually, that's stated too strongly. The players ability to move from passive user to creator is curtailed through the filter of the DM's views. So long as the player stays within a certain boundary, then he can be as creative as he wants. If the filter is too fixed though, if it is too fine, then the player has little or no choice to become a user, rather than creator.
OTOH, mechanics issues, beyond the player deliberately attempting to abuse the system (which is a separate issue), are much more concrete. As the DM, you can point to mechanical elements in the campaign that will conflict with the mechanical elements of the player's idea. Take psionics for example. It could very well be that the DM doesn't have any idea how psionics works and has no interest in it. Since psionics does require the DM to be somewhat proficient with the rules, this becomes a problem. Additionally, the DM may not want to use psionic monsters since it adds so much complexity to the table. A reasonable player can usually see how this could be a problem.
I recall another conversation about warforged where one DM talked about how they would not fit into his jungle based campaign. Mostly for the same reasons they don't fit into my WLD game - a number of themes and challenges get tossed because of the mechanics of the WF.
Most players IME, are willing to concede that the DM shouldn't have to rewrite his entire campaign to fit a new PC, or whatever mechanic.

Conflicts that are based in mechanics are, IME, better reasons for disallowing elements. Conflicts based purely on what the DM feels is the "feel" of the game are so subjective that it becomes much more difficult to build consensus.