Far from viewing Jefferson as a skeptical but enlightened intellectual, historians of the 1960s portrayed him as a doctrine thinker, eager to fill the young with his political orthodoxy while censoring ideas he did not like.
e. e. "far from") "viewing Jefferson as a skeptical but enlightened intellectual".
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In this sentence "far from" means something a bit like "rather than", but more strongly emphasising that what the historians actually did, i.e. "portrayed him as a doctrine thinker", was entirely different from (i.e. "far from") "viewing Jefferson as a skeptical but enlightened intellectual".