Her story is completely sad. Because she deserved her vengeance. She was born with strong psychic powers and her father wanted them. So he had her experimented on since she was a little girl and kept her in isolation. When she grew old enough to bare children, they had her impregnated so her son could become a super soldier for them because he inherited psychic power from Alma, his mother. So yeah, they deserved to get what was coming to them.
The little girl that you see throughout the game is Alma's true self, psychologically. It's her consciousness manifested into a visible entity.