The most common and most likely answer to this crossword clue is the 5 letter word BIGOT
I've seen this crossword clue in Independent
B
I
G
O
T
More clues leading to the result BIGOT
- Regularly being most intolerant, him?
- Chauvinist's piece about good love
- One with unpleasant views returning to Gibraltar
- Leave boring part for sectarian
- Important part of bible for homophobe?
- One with fixed views of large part of bible
- Racist piece about to be removed
- With generous spirit not present, heartless? I am
- Character lacking tolerance from great books
- Run, in part, as epitome of intolerance
Buddy explains!

The straight part
We know that "sectarian" is the straight/definition part of the clue. The straight part is often a synonym or definition, in this case sectarian = bigot.The cryptic/wordplay part
In cryptic crossword there's often an wordplay/cryptic part as well.This part involves a more complex hint, such as an anagram, homophone, hidden word, etc.
Sadly, We don't have an explanation for this specific crossword clue yet.
What does BIGOT mean?
BIGOT noun- One who is narrow-mindedly devoted to one's own ideas and groups, and intolerant of (people of) differing ideas, races, genders, religions, politics, etc.
- One who is overly pious in matters of religion, often hypocritically or else superstitiously so.