Yes, Menecin’s greatest fear has to do with Naiore, but it immaterial to him at this desperate point whether or not she had ever loved him in return. Rather he is feeling the full weight of responsibility for her. In those early days he saw her keen mind and judgment of character and so had encouraged her, believing that she might rise to be something more benevolent that what she has ultimately became.
In his eyes he feels that he chose to turn his back on the truth and now views his own love for her as major weakness that has had resulted in the horrendous suffering of others. Seeing this ‘bigger picture’ he is laboring to cut off that love from his consciousness the best he can, (even though those early days with Naiore are still very fresh in his mind), so that he can end this permanently.
I suppose his greatest fear is that he will be unable to, or be prevented from carrying out what he sees as necessary, and that Naiore will continue to grow even more degraded and debased from his memory of her. He is troubled by his oath, but no longer feels he is of value since he has failed at every point. And his last hope of taking her east he has finally realized is not possible or practical. So he has resolved to sacrifice himself and her, in order to set things right again.
Don’t forget though, that he has also vowed to Vanwe that he would not lose her, and that might be a way to reach him.
I don’t know if this helps. I hope it does, and that it doesn’t make things more difficult for you. There is nothing deeper going on, unless you have a suggestion. In which case I'm all ears.
(And teeth apparently too!)