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In the Season 5 finale, Jacob looked at Ben and said, "What about you?" The look in his eyes could have been interpreted as sympathy or disdain. It could be sympathy for a man whose actions indicate an unfeigning faith. But it could also be disdain, for one's enemy.
When Ben was shot by Sayid, he was taken to the temple to be "healed". If this "healing" took place at the hands of the smoke monster, a number of possibilites exist.
1) Little Ben died and the Ben we see now is Nemesis or Smoke Monster (unlikely)
2) When Richard said that Ben would never be the same-- that his innocence would be lost, it implied that Ben was forever connected to the apparent dark side (more likely)
3) Or, as is usually the case in Saviour-types being killed in literature, he was goading Ben to kill him, because he knew he'd be even more powerful, once freed from the chains of this physical body he was in (also likely)
I guess we'll see...