I was surprised to discover that "honcho" is Japanese (班長, or team leader) in origin. I thought it was Spanish. In English, honcho is a noun, meaning boss or leader. It is sometimes a verb, meaning to lead or manage. Honcho is not typically an official title. It is informal and familiar. It is not necessarily pejorative - in fact, its informality often suggests an ability to make progress rapidly, without waiting for bureaucracy. However, the writer of your phrase probably is using the informality of the word in a satirical way. The Scientology folks often take themselves very seriously, so referring to their leader as a honcho is ironic in tone.