Judging by Matt Nix’s comments at San Diego Comic-Con, The Gift will take place in a stream that won’t necessarily be affected by what happens in the films.
That movie did establish that different things happen in different streams without necessarily impacting the others.
The X-Men universe on the big screen was never the most straightforward place, and things just got more complex with the timeline shenanigans of Days of Future Past.
Considering the way shows like Agents of S.H.I.E.L.D. have had plots dictated by the events of movies, I’d say that Gifted existing in its own stream will be a good thing.