I find it amusing how no matter what whichever character linked to that name in the Comics came first will be the last to appear in their respective Cinematic Universe.
The DC owned character affiliated with the name Captain Marvel came way before, being a Golden Age character. He no longer goes by that name now thanks to complicated trademark BS but he will always be Captain Marvel to me. Marvel's Captain Marvel will be getting her film before Shazam (but still not before Wonder Woman, DC is beating Marvel to getting a Female lead film out even though Marvel had a huge head-start).
With the characters known as 'The Enchantress" it's the opposite. Thor's nemesis/love interest Amora came first in the comics, but DC's June Moone will be appearing in Suicide Squad in 2016. Amora isn't likely to appear any sooner then the next Thor solo film now slated for November 2017, and there is no confirmation on that even. Marvel has no excuse for this, she should have been in the Thor franchise by at least the second film. If she's not in Ragnorock I'll be pissed, I may even not see it over that, by then I'll be having more then two Marvel and one DC films a year to hold me over, so I probably will start opting out of some Marvel ones.
If Amora is in Ragnarok they'll probably never call her Enchantress. June probably will be, the code names are likely part of how Task Force X operates.
So the chances of audience confusion are pretty low. Still, I find it amusing that this is how things are playing out.