The historical awareness you mention is how I was able to accept Sisko's line, which I initially found jarring as well.Certainly, Sisko has always, even before his experiences in the past, been a character in touch with his cultural roots. We can see it in the foods he likes to cook, his collection of West African masks, etc. My problem is not that Sisko finds fantasies like Vic's distasteful for what they conceal about the historical reality--I perfectly well sympathize with that attitude--but with the fact that the dialogue seemed to imply (to me, anyway) that the concept of race had persisted even into the 24th century.
Having a father who instilled a love of traditional cooking in him and can quote the Bible probably helped (I always thought that the Sisko family's preference for Old Testament names was also a reflection of that sense of the past); Sisko is not only unusually aware, but also sympathetic to those historical realities. I imagine the reason for his vision of life as Benny Russell took that particular form is because it would speak to him in a way it wouldn't speak to someone else (like Kasidy, for example, who wasn't bothered by Vic's the way he was).
It seems like Star Trek characters are free to "borrow" bits and pieces of each other's cultures while still maintaining distinct cultural identities, so I tend to think of Sisko's perspective as being the same as Chekov's ability to be culturally Russian, or Picard's ability to be French, without affecting their perception of themselves as humans.I suppose, to me, that the litmus test would be whether race still serves as criteria for these future communities, or whether individuals of any given ethnic background could claim appartenance to a cultural milieu, without a biological factor, merely because it is the culture they prefer. I think we can see that to a certain extent even today, although individuals who might prefer a culture other than the one they were born into still face a lot of prejudice (with epithets like 'poseur', 'coconut', etc.; and it doesn't even have to be racial: even I sometimes get flak from my more fanatically francophone extended family for being far more engaged in anglophone culture).
As you said, that tension can still come up at any point where a dividing line has been drawn...