I don't think the new Star Trek should be segregated; but on the other hand, I do think that it would be best.
I believe those who prefer the previous continuity would be overwhelmed by the posts about this one; it's not unreasonable to suggest that some might even go as far as to continue the argument about which is best, perhaps even in an unseemly, inflammatory fashion. Not everybody can handle being a minority.
I'm not saying everybody is like that; on the contrary. But those who refuse Star Trek and, perhaps, adhere too much to the old one, are much louder then those who love both. It might be best to spare any new fans from that, lest you scare them away faster then they came.
Not only that, but -- I don't speak for them here; just making an assumption -- I'd think they wouldn't want Star Trek intruding upon their old love, either.
So it might be best for both sides.
Of course, when all the commotion does eventually die down -- as I believe it will, eventually --, it's another matter. When the staunch proponents of one of both, who exclude the other, aren't as loud any longer, there's no reason to continue a separate forum. It's all Star Trek anyhow.