I have the impression that the timelines are entirely different. If they did diverge at some point, it was independant of the events on-island. Jacob's touch probably doesn't have anything to do with the divergences either, given the differences in events that happened before Jacob even touched the candidates, like Sayid getting his brother to marry Nadia. Or Locke still being on talking terms with his father (which leads us to the question - why is he in a wheelchair in the Sideways world then?)
I'm not sure Jacob and Smokey are going to be very clearly-cut good guys and bad guys, my impression is more that they just champion free will vs. fate. And of all the encounters Jacob had with the candidates, only in Sawyer's case can you say he nudged him. And if I remember correctly, at the same time he gave him the pen he also said not to be angry or something like that, so again, offering both possiblities.