“Shepherd” isn’t his name, either. It’s a title.
Mal: You a Shepherd?
Book(surprised): I thought the outfit gave it away.
The clothes he was wearing were common priestly/pastorly apparel.
Yeah, “pastor” pretty much means “shepherd”, anyway-- They just use a different word in that 'verse. It’s basically the same thing as Battlestar Galactica using “So say we all” instead of “Amen”.
“That ain’t no Shepherd.”
Your partner is correct that Book dies, but not where. I’m assuming by “the secret colony” you mean Miranda, the planet where the Reavers were created. Book died elsewhere, before the crew visited Miranda. (Book’s was one of the towns that was destroyed by The Operative in order to give the crew no place to run to–he died in Mal’s arms, more or less.)