The director of operations for an obscure but wealthy ­Beacon Hill church stood ­before a federal judge Wednesday, accused of raiding the coffers of the congregation where he said he found redemption and enlightenment.

Federal agents arrested ­Edward J. MacKenzie, a 54-year-old self-proclaimed henchman for mobster James ­“Whitey” Bulger, after he was indicted by a grand jury on charges of racketeering, extortion, bribery, and money laundering.

MacKenzie, who lives in Weymouth, started working at the Swedenborgian Church on the Hill in 2003 and immediately began scheming with coconspirators, according to his indictment. Their alleged goal was to “obtain power and influence” and use both to “defraud the church of its considerable financial holdings and profit.”