Someone once asked...
Someone answered with kindness...
Burnout is extremely common in those pursuing doctorates and doctorial work. It is a thankless field, and academia is a minefield full of large egos, deadlines and bureaucracy. The issue here is that quitting results in a zero, all of the effort and time spent already will evaporate. She may no longer be interested, but she found the strength and courage to go through two years of the grind towards the doctorate. She might be losing it mentally, on the edge of burnout, but it is now your job to support them. Not words of encouragement, but things that actually help them. Maybe she loves whole wheat toast, with Swiss-Loraine cheese, and a sliced tomato. That tiny thing, just bringing her lunch while she's completely overwhelmed might make a huge difference. With two pairs of hands, scaling the mountain becomes easier work. Not easy, but easier.
Another soul answered...
You can honestly tell her that no matter what her decision will be you will support her on the journey. And then you do support her. That would be the best shot for her to make decision herself, ultimately it’s hers.
Another soul answered...
I know at least a dozen people with hard science PhDs, and maybe three who don't have lasting psychological damage a decade later from the degree. Your partner is the only person who can decide if it's time to change course. I would recommend making sure she knows that not finishing is an option and that she loses nothing in your eyes if she ever decides to take that path. Also very important: sometimes, the way the move forward in a PhD isn't by moving straight. People I know who took a break to recover their sanity or changed their topic partway through extended their process, but losing your mind before you finish has a tendency to extend the process as well.
✦ This sign has found its fate.