http://wow.gamepedia.com/Summoner_Nolric is a high elf warlock trainer whose eyes aren't green despite by definition having to channel fel.
Not sure in-game examples are good enough proof for that kind of stuff though, and lorewise, I'd assume Nolric would have fel-tainted eyes.
A Blood Elf is someone who renamed themselves in honor of the fallen 90% of their population, so it's entirely possible that there were some untainted. I imagine so many Blood Elves have green eyes because until Rommath returned to Quel'thalas and reclaimed much of it from the Scourge with the awesome power he and his magi had attained through fel, Silvermoon must have been one of the only safe places around, with a high concentration of elves to defend it. Then when Rommath showed up and repaired it with fel fueling his magic, it tainted lots of people.
There is also a blacksmith in the Blood Elves' base on the Isle of Thunder that has blue eyes, so there are a few examples to support that.
I just don't think it's a standard that all Blood Elves will have golden eyes in the near future.
Liadrin sure, as she seems as much a paladin now as Turalyon or Uther (the most well-known glowy-eyed paladins) ever were. Other Blood Knights maybe. But all Blood Elves? I sincerely doubt it. At least not for a really really really long time.
Also, Elune didn't uplift the Dark Trolls into Night Elves. The Dark Trolls mutated through prolonged exposure over a period of years, perhaps even millennia, after they settled around the Well of Eternity, which, is not made of Elune or anything like that. I believe it's the blood of Azeroth after the Titans ripped an Old God from the ground, or blood of the titan sleeping inside it, if it's been confirmed that there's a titan inside Azeroth. I don't remember.