Many of the large brasseries (like Bofinger or the Wepler) have non smoking areas, but I can't vouch for their not being next to a smoking area. Many times it's a question of space, most restaurants not being large enough to make an effective distinciton. The Morosophe in the 17th has a non smoking side.
I know there are a few completely non-smoking restaurants in town (an Italian place in the 18th-- can't remember the name; Robert et Louise in the 3rd, most vegetarian restaurants...). I seem to remember that the Zagat's guide for Paris lists restaurants that are non smoking or have a real non smoking section.
Some useful sites:
http://www.droit-air-pur.com/nosmokingrestaurants.htm
http://www.paris-marketplace.com/pag...eId=306&page=1
http://www.smokefreeworld.com/paris.shtml