On the game files, there is a file named "DataIntegrity.rvdata2" which is formed the second you start the fight with Megan, not during the intro cutscene. Delete it if you dont want to have the scene where Megan basically drains you and resets your levels.
As for fighting her, you would need to be level 30 minimum to even withstand her attacks. Also try to get as much equipment as you want. IMO, i just cheated on and put myself lots of gold to get the best equipment and spam the trainer to get enough levels (cuz i needed to test stuff). I say it does take a lot of grind to get to the point of that normally