Joan of Arc didn't actually refuse to wear women's clothing. Her captors stripped her down (she had been wearing a dress) and left her naked with a pile of men's clothing. She had most likely been raped repeatedly, and since her choices were (1) put on men's clothing, or (2) remain naked around a bunch of English rapists, she took the first option. I have yet to read a book or see a movie about Joan of Arc that left this part out.

The clothing thing was just another excuse to burn her. She was killed because the English and the Burgandians wanted to deliver a blow to Charles VII of France by slaughtering the hero of his people. Incidentally, their little ploy didn't work. Charles succeeded in winning back most of France from the English.