I doubt it. Unless they are going to completely re-write history and remove her as the mother of Jim's future children.
DC completely rewrites history all the time, and Barbara Kean is no exception. The character was originally introduced in an alternate-universe story as Jim Gordon's fiancee and the implicit mother-to-be of Barbara "Batgirl" Gordon (hinted at because she was a redheaded librarian). When she was added to the then-mainstream continuity in
Batman: Year One, she was the mother of Gordon's son, later established as James Gordon Jr., but due to the chronology of BYO, it was later established that Babs/Batgirl was actually Jim's
niece (his brother's daughter, I think) whom he and his second wife Sarah Essen adopted. It was subsequently retconned that she was Jim's biological daughter through an affair with his sister-in-law, but I'm not sure that stuck, since
the current DC wiki entry for the pre-2011 version of Barbara Gordon gives her parents as Roger and Thelma Gordon.
As of The New 52, however, she's been retconned back to being the daughter of James and Barbara Eileen Gordon (whose maiden name is unestablished) and the biological sister of James Jr., with no Sarah Essen in sight.
So Babs/Batgirl has had multiple different parentages: James and Thelma Gordon
from 1967-1985 (more or less), Roger and Thelma Gordon (biological) and James and Sarah Gordon (adoptive) from 1985-2011, and James and Barbara Eileen Gordon from 2011 to the present. So there's no way in which Barbara Kean is immutably required to be her mother. Barbara Eileen (who seems to be the same character as Barbara Kean) was James Jr.'s mother in both the post-Crisis and New 52 universes (New Earth and Prime Earth as the wiki phrases it), but James Jr. didn't exist as a character prior to
Batman: Year One.
So really, the producers of
Gotham aren't locked in at all when it comes to Jim's future family. They have various options to choose from within the comics, and they could invent their own new version as well. For all we know, Leslie Thompkins could be Barbara's mother in this universe, if the producers feel the chemistry between McKenzie and Baccarin is strong enough to add her as a regular.