Your darkside gained a sentience of its own when you gained the soul crystal, or at least over the course of the 30-50 quests of it. Really though the whole thing with Fray is the sort of thing thats mind screwy to begin with.

Personally I take it as, you don't need Fray anymore (if you ever truly needed them to begin with), but that doesn't mean they dont matter, just as all the lives you touched that even when you didn't know them and even when you had negative times with them. Its very possible that Fray won't show up in future DRK quests (and the next set will most likely be about Sidguru and Rielle regardless) but whether you choose that to mean Fray is gone for good or just now peacefully a part of you is, well, up to you.

Also as an FYI the very final journal entry notes that the "Esteem" we can summon starting at lvl 80 is NOT our Fray, just a little trick we managed to learn.