When the crime was reported, an investigation was started promptly; the accused officer was suspended; and upon the conclusion of that investigation he was charged, arrested, and is now in jail. It seems like the process worked exactly as it should here.
Was such criminal behaviour condoned (tacitly or otherwise) by the department? I've heard stories about this happening in the past, but there's no mention of anything like that in this article.
Was the department aware of prior complaints? It doesn't seem like it; while the article implies that this was not the first assault committed by this officer, the DA's investigation clearly wasn't able to uncover evidence of any prior complaints, and for all that police officers have a reputation for standing together I doubt they would bury complaints against a known rapist that effectively.
A crime was committed, and the criminal went to jail. How does the criminal's employer come into the picture?