He had to to keep her from burning up and dying as a result of the Meta-crisis. Her human brain was unable to long sustain the vast knowledge, powers of perception, and intelligence of a Time-Lord, and it was killing her. So, the Doctor erased her memories of their time together to save her life. With this, the Donna Noble she had become died that day. Also if she remebered her travels with the docotr even for a second she would burn up.