So far as I know there is no controversy, just wrong assumptions by people who don't know the history. There was a contest between cities on which one the county would be named after. Orange and Santa Ana were the two finalists. Orange was given the honor, and Santa Ana the county seat.
Apparently, the county web site thinks differently, but I believe that is what happened. (The city of Orange, was named for the orange groves. The county of Orange was named for the city.)
My family has lived in Orange County since the 1920's and I myself since 1957. First time I ever heard that story. It does not appear either in the County's historical portion of its website nor the City of Orange, thought the latter does mention the fact that Orange was originally called Richland. Any source for the story beside your own belief? When did this contest take place?