Is the difference of opinion among the girl's family regarding a suitor, and the fact that he smokes, an indication that Salat al-Istikhara was not accepted?

As long as the young man is upright, of pleasing character and religiosity, and has promised to repent from smoking, and you have felt reassurance after performing Istikhara, then proceed with this matter, relying upon Allah. The prescribed action after Istikhara is to go forward with the matter; if it is good, it will be facilitated, and if not, it will not be facilitated. The disagreement of some of your family, who hold a different view, does not harm.