We don't know how important Enchantress is in the greater scheme of things for the DC universe. They may have chosen her so she could die in Suicide Squad because she is a lesser known character. Or she could be a tie to magic and the supernatural in the shared DC universe. Whether she appears in other movies or not, what she does signify of course is that there is magic and the supernatural in the DC movies, and opens up that aspect of things.
Wonder Woman, as the daughter of Zeus now, has the gods of Olympus as her villains/supporting cast. While I do expect magic and the supernatural to be a part of WW's world in some way, there are many ways they could go for her first movie. The fear I have is that WW fighting a witch or sorceress and magic being the main threat could make it yet another 'Supergirl' movie. There's always the temptation for female-led movies to have the heroine just fighting another woman and focusing on magic. While those elements are expected to be in a WW story at some point, magic and/or the supernatural can be present the way it is in Star Wars or Game of Thrones, where it is always around but not always the focus or so blatant. The more blatant magic I would expect in a Justice League Dark movie.
I don't know, Enchantress in Suicide Squad will have to be presented in a way where magic can help out the team in certain ways, but not be the easy answer to save the day.
I guess I wouldn't mind her in a WW movie only if there is more to it than WW vs. an evil sorceress.