Janeway was responsible for the death of the Doctor's holographic daughter
This was during a time when she had her internal debate about whether or not he could be treated like a sentient being.
B'Elanna added the RNG subroutines to counteract the diabetic, sugar overload program he originally wrote. She was at least trying to give him a realistic family experience.
Janeway was just tired of her computerized doctor wasting time and literal energy with a synthetic family. She added one more subroutine, kill the daughter in a fashion that current Federation medical science can't fix.
The Doctor would be too sad to go back and she can return to tutoring those Victorian-era kids while fucking their dad.