The role of the courts, as you describe, is to remove the ability of the traditionally-powerful groups to exclude members of traditionally-underpowered groups. For the reasons I described above, it doesn't work the same way in reverse; you can't take away the power of underpowered people to form communities, because that's not a power they've traditionally held.
As far as the question of health goes, I'd say yes, it's extremely healthy for groups who have been denied power by existing systems to meet and organize in exclusive groups where members of the power structure are not allowed in. Members of the existing power structure will, inevitably, work to promote the status quo, even if they're not necessarily aware they're doing it. (This is perfectly understandable, of course; people like being in power, and there's no reason they shouldn't.) Underpowered groups need to be able to organize free from the influence of those who would, even unintentionally, undercut their efforts to empower themselves.
Also, I'm of the belief that if people were really interested in forming "tidy little like-minded tribes" we would have done it already. After all, we've had hundreds of thousands of years to put that into effect--and, depending on how you believe human beings came into existence, it could be argued that we started in tidy little like-minded tribes, and have worked our way away from that state. Sure, people like being around other people like them; it makes it easier to communicate, for one thing. Plus, there's (again, if you believe in such things) an evolutionary imperative to associate with others who resemble you; people who are "different" could potentially be threats, or at least could compete for available resources. We're a tribe-minded species to begin with.
But the impetus of history seems to indicate that people move away from that status rather than towards it, on a societal level; people interact, interbreed and interchange ideas, and with the development of the internet that's easier than ever before (for a certain value of "interact", anyway). As such, I don't think the human race is in any danger of become isolated tribes; rather, disempowered groups are having opportunities to seize greater power, shake off oppressive systems and change existing power structures. It's a gradual, painful process, and it ain't going to wrap up neatly in any of our lifetimes, but one of the early stages of that process is the ability of members of these groups to congregate exclusively.
A long-winded answer to a fairly simple question, but hey, it's the internet, after all.