There are quite a few restaurants springing up which are smoke free. Try Tibits or Hiltl (both veggie restaurants), there is also a noodle bar at Kreuzplatz.
Pubs tend not to be smoke free yet but then again, they aren't really any place for a baby anyway.
As for cinemas I certainly couldn't imagine taking a baby to a 2 or 3 hour film even if it were allowed. What would you do if he or she suddenly decided to have a crying fit? If memory serves me right, babies do choose a supremely unsuitable moment to let rip with a massive cry. Mine is three years old and this rule still applies...