I think the principle of shunned outsider is ok but in case of Barnabas, like somebody already said, he's running a black market, his prices are inflated and I think it's quite clear he's not an honest, good merchant in a peaceful town.
More a greedy kind of fence or other peddler of stolen goods, in a shady town full of bandits, muggers, thieves and assassins, only interested in making gold.
He doesn't care where it comes from, will readily buy or sell corpses of bandits and whatever belongings they drop after the PC kills them.
Granted, other shopkeepers don't mind that either but for the sake of argument, I'm pointing out that alignment seems to be of zero relevance here, all that matters is profit.
It would be thematically proper if CKs could trade with this single merchant and nobody else.