A brilliant young woman-of-science disguises herself as a (male) witch-finder’s assistant so she can undermine the brutal practice of witch burning in spite of a greedy witch-finder who will not pardon any of the town?s witches. A musical comedy

Rather than "Woman of science", just say "A female scientist".

And where and when is this set?

>>>" who will not pardon any of the town?s witches"

In other word's, he's merciless.

The logline should frame the plot as a conflict between two people, ?the woman and the male witch-hunter rather than as a conflict between a woman and the practice of witch burning -- and, oh, by the way, the prime instigator of the witch burning is a witch hunter. ?Establish a direct protagonist vs. antagonist relationship.

You should make it personal.
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"When her sister goes on the run after accused of being a witch, a woman of science disguises herself as a preacher and joins the hunt led by a famous witch hunter to throw them off the track."