Yeah the Logan stabbing her thing has always bugged me that he got a free pass on that. He has a damn adamantium skeleton, just hit her on the side of the head with his fist and she is out cold, he didn't need to gut her. He was saving Selene, an actual real mass murdering psychopath mutant vampire, and gutting Rachel to save Selene. What the heck. When I originally read the comic where she got written out it was actually really upsetting and no one looked for her or tried to locate her after.
I wish they had used her more as a secondary character on Cable after he rescued her. Heck I have wanted for ages that they pair Cable and Rachel on a comic together. Have him pull her into his timeline and she becomes his backup on all his missions going forward. It removes the parental complication for a while and lets the brother and sister pair shine as a partnership. I wouldn't even mind it if Cable and Rachel end up doing something together that pisses off the X-Men in order to save the timeline. Like showing up during a battle and outright killing one of the threats, this is something Cable has always done, but I wouldn't mind it if they had Cable decide to pull Rachel directly into his missions with him. She needs a new direction and Cable could use a supporting player in his ongoing appearances.