no, they did not. no scientist was ever executed for stating that the earth was round. no scientist was ever excommunicated for saying it was round, either. by the advent of christianity, a spherical earth was common knowledge. dante alighieri even alludes to a spherical earth in his divine comedy.

giordano bruno--a mathematician, philosopher, and astrologer--was executed by the church for heresy, a part of which involved his belief that the sun was one of many stars moving through space.

cecco ascoli, a physician and poet, was executed by the church for attempting to uncover the birthdate of christ by reading his horoscope.

marco antonio de dominis, a "man of science" according to wikipedia, died a natural death while imprisoned by the church for his political attempts at reformation and his published works denouncing the church.

galileo galilei died of natural causes under house arrest for the heresy of suggesting that the earth revolved around the sun. he continued to research and publish until his death.

these men are about as close as you'll get to a scientist being executed by the church for anything.

http://en.wikipedia.org/wiki/Giordano_Bruno

http://en.wikipedia.org/wiki/Cecco_d%27Ascoli

http://en.wikipedia.org/wiki/Marco_Antonio_de_Dominis

http://en.wikipedia.org/wiki/Galileo_Galilei

edit: added galileo, after it occurred to me that if i were going to mention de dominis' natural death while imprisoned, that i might as well mention galileo's natural death while under house arrest.