From reading what Tom28 said, to me it says that Tom28 is unhappy with one aspect of his sensei's behavior. Therefore, Tom28's goal is to change the dojo into what he feels is best. For me, I see that this is the real issue and what to focus on in the thread, does Tom28 (or anyone) have the right to achieve his goal for the dojo?...
I see what you mean...that's a weird issue. On one hand it could be something (to use egregious examples) like "OMG I hate all that bowing and Japanese language", and we'd probably all agree that the member trying to change the dojo is way out of line. But on the other hand it could be something like "wow that's the third time this year year sensei broke someone's arm because they weren't being responsive enough uke", and most of us might think that that sort of thing should change. So much behaviour is not so obvious though, and, as you rightly point out, may or may not be in the eye of the beholder.
I think that a member of even so starkly hierarchical an organization as a dojo has a right to agitate for a change that they feel strongly about. What if, for example, your sensei is Japanese, and makes it clear that he expects the female students to keep the dojo tidy and launder his gi. I would feel comfortable confronting him about that. I wouldn't be weird about it, or leave in a huff right away, but if he were unable to change his attitude about that I would leave eventually after trying to change the dojo.
To return to Tom28's problem, if he truly believes (and it's certainly his duty to be certain and not to jump to hasty conclusions) that the instructor is acting outside of the boundaries of good behaviour, I would support his right to try to change the culture of the dojo. If he is totally wrong about the situation, he'll leave and nothing will change. If not, then maybe others will agree with him and the dojo will try to change (or split, like John Burn's situation).