This is not some general diatribe about strong women
In this game's story it's a fact she was holding him back. She was an easy target and a ruthless opponent took advantage of that. After that she was even weaker than before and obviously even more at risk. Unless the whole game is him playing bodyguard, she was an obvious achille's heel for MC.
It's not a novel concept really, why do you think so many fantasy heroes have secret identities? Because it's easy to take them out by targeting their loved ones.