I kind of like the idea OP.
Another suggestion would be that these naga are actually kaldorei who, during the War of the Ancients, managed to get to the Well of Eternity.
When the area sunk, they didn't have time to flee. When the Old God gave Azshara the choice and she accepted, he didn't stay to make a difference between some elves and the others, so turned all into naga. Out of shame, the kaldorei resistance being turned into naga stood there and, thinking they were punished by Elune by getting this form, fought Azshara and her naga. This would explain why naga haven't surfaced so much until now for the last 10k years.
However, as time passed their numbers started to fall. Now they're only a few thousands left, not enough to fight Azshara and her minions. That said, they decided their only choice is to reconnect with their culture, the kaldorei, the night elves. At first, the night elves were distrustful, so they bring a gift, some artifact. This makes the night elves accept them, as they accepted the good erredar, the draenei, even though still suspicious.
Kind of like "keep your friends closer and your enemies closer".
The naga rebels also had a culture shock seeing how different the night elves became, so they're also somewhat distrustful of them since they are scared the night elves might try to impose their culture on them, something they disagree. Both still worship Elune, and the females are considered stronger, but here the similarities end. The naga still have a sort of monarchy with a Princess of sorts leading them, they use arcane and fel magic openly, they have shamans and don't really care as much about the living things unless it affects them.
---------- Post added 2012-10-30 at 01:03 PM ----------