Because the Janeway we follow in Voyager didn’t go back in time. Admiral Janeway did.
People are shaped by their experiences and their choices. Admiral Janeway had many experiences and made many decisions that we know nothing about. It led to her becoming who she is but she wasn’t the main character of the show. The character we followed was Captain Janeway who was immediately opposed to the idea. Actively fought against it. She was eventually broken down but honestly by that point the damage had already been done. There was little that Captain Janeway could have done to prevent the Admiral from doing what she was doing.
Also Admiral Janeway effectively eliminated the Borg. I give her brownie points for that.