I watched this anime 3-4 years ago in which a super girl is beating some guys but accidentally kills an innocent boy. She then merges herself with the boy until his body is properly restored.
Might you be thinking of Birdy the Mighty?
Birdy Cephon Altera is a Federation agent chasing interplanetary criminals to the planet Earth. While in pursuit of one such criminal, she accidentally kills a high school boy named Tsutomu Senkawa. However, there is a way to keep him alive. He ends up being merged into Birdy's body and must remain so until the repair of his body is complete.
So, Tsutomu is stuck sharing a body with an attractive, strong, and impulsive space police agent while trying to keep his family and friends from finding out about Birdy. In the meantime, Birdy continues her investigation. Together, they take on a secretive group of evil aliens planning to perform experiments on the unsuspecting inhabitants of Earth.
It's based off a manga. There was both an initial OVA of four episodes in 1996, and a follow-up TV series, Birdy the Mighty Decode, which aired 26 episodes from 2009-2009.
Found by searching for anime superpowered girl merges with wounded innocent, which led to this forum topic.