In the context of ancient China times, and in a fantasy novel, where people collect disciples for martial arts and whatnot. Would xx sect be better or xx school? Or even xx faction instead of those two?
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宗门 is a buddhist term, the more general word is 教派 or 宗派. If your setting is buddhist, as most martial art is, then you should most likely use buddhist concepts.
Otherwise people tend to use 家 to categorize different schools. Sect and faction are more narrow concepts, just as in English, and can have negative connotations.