Harley Sawyer technically never did anything directly or intentionally to the protagonist at all.

I think Craster from Game of Thrones/A Song of Ice and Fire also qualifies. While Jon Snow and Sam Tarly are both disgusted by his practice of raising his own daughters as sex slaves and sacrificing his own sons, they never confront him directly while he is still alive and, if anything, they are technically allies because their Lord Commander has made an alliance between the Night's Watch and Craster.

Thanks, guys. It's good to know.

I do think SpongeBob from the Bikini Bottom Horror could count as the only protagonist SpongeBob gets against is Sandy, but that's about it.