In my opinion, it would not be illogical for her to be a Loa. Troll Druids and Troll Priests for example mean it would not be illogical. Also lets not forget the origin of the Night Elves. They came from trolls(Who all worship Loa's)
Though it's speculated that E'Lune might be a Naaru why are the Night Elves more nature like? Look at the Draenei and their way of life, it does not match up with the Night Elf ways at all.
Now lets think of her role in the Night Elves lives. She has been with them for thousands of years giving the Night Elves a big advantage over certain things. Why would some Naaru do this for the Night Elves and the Night Elves only? And why would the Night Elves have a completely unique. The only sort of deities that have unique powers in WoW are the Loas.
I personally think that it would make sense for E'Lune to be a Loa. This is speculation and yes I admit some of it is pretty widespread but can you think of another being that would give favor to just one race(Possibly two)? I think one reason why this theory gets blown to the ground is the fact that there was quite the outcry at it being confirmed the Night Elves coming from trolls. The players would crawl to the Blizz HQ and beg them to change the lore if she was a Loa.