Actually the Naga are generally more closely related to Blood Elves then Night Elves. Both the Naga and the Blood Elves are descended exclusively from the Highbourne Night Elves, while only a small percentage of modern Night Elves are (and the few that are have only recently joined the Alliance).
Should Blizzard ever decide to make the Naga playable, Blizzard could choose to emphasize their connections to the Night Elves and make them Alliance or their connection to the Blood Elves and make them Horde as they see fit.
Of course at the end of the day I'm not sure if the technical problems facing the Naga (namely the ability to ride mounts and not look awkward as hell) can be realistically overcome. I'd even go as far as to speculate that the Jinyu may of been introduced partly because they are an aquatic-themed race that doesn't suffer from the Naga's technical issues.