A little late, but hope this helps:
I had Karabiner Elements working great to reassign the eject key and disable the current one with Sierra on my older Mac Pro - until a recent OS update. I assigned the F6 key to "eject", and that disabled the regular "eject" key. Karabiner also had a recent update (a couple days ago) that appeared to default all my keyboard mods back to standard Apple. Went back to an earlier version in backup, and it didn't fix the problem. Now, I still assign the F6 to "Eject" (and it works fine there), but the "Eject" button is no longer disabled. Did a lot of searching on the net and it seems that Apple has us on this one for now. At this point, I might try making a cover that fits over that corner, so when I accidentally hit the key, it doesn't work.