Crossover's dark future may yet come to pass, so it may not be an alternate future at all.
I think you mean
Crossroad. I always interpreted Chapel's actions at its end-- where she elects to stay in Starfleet and attend the Federation Science Institute, as killing off the Consilium future. In the timeline the future-people report on, she went to the Institute of Xenobiology.
Inspired by the recent discussion of
Crossroad here, I re-bought it last week and just finished reading it for the first time in many a year. I'm surprised I ever parted with it. It's a good book, with interesting ideas and some nice lower-decks texture to the depiction of shipboard life.
As for Chapel's action at the end, I'm not sure which future it implies. After all, "Federation Science Institute" sounds like a civilian institution and is described as a university. The Institute of Xenobiology could be a department of the FSI. (Although we do know she returns to the
Enterprise in TMP.) Also, the characters from the Consilium future know about the first Klingon in Starfleet serving aboard the
Enterprise-D, suggesting that TNG is in their past.
However, the future timeline depicted in
Crossroad must be an alternate from the one that now exists in canon and books, for two reasons. One is that the Consilium-era Federation doesn't have quantum slipstream drive; they went right from warp to psion drive. The other is that Romulus wasn't destroyed in 2387. Perhaps in that timeline Spock was able to save it in time.
I think the Consilium future could be an extension of the "Before and After" timeline. In that future, Kes never left
Voyager and Seven never joined, so the events of "Scorpion" must've happened differently. So in that timeline, "Hope and Fear" might not have happened either and
Voyager wouldn't have gotten slipstream drive.