After rewatching this season and many of the old episodes on DVD, I have developed a theory about Locke and Ben, why Locke can walk on the island and why Ben ultimately killed Locke. Here goes...
I think that Locke died immediately in the initial crash of flight 815 and from the start of the series he was "dead" however his body was immediately taken over and used by MIB/smoke monster the same way that Flocke is now. This would explain how Locke went from being paralyzed in the wheelchair to suddenly being able to walk around the island.I don't think we ever saw the real Locke on the island, only in the Alt universe.
Other evidence for my theory - Locke was seen early on walking around with "the knife", which I believe is the same one that keeps reappearing throughout the series. Locke was also the one who knew about the backgammon, black/white rocks, Adam/Eve in cave, etc.
Now regarding Ben - I think Ben is basically good and that Ben is trying to protect the island and save the world by keeping evil from escaping from the island.
Now, here's the tricky part - I think that when Locke left the island the first time, it was actually really Flocke (MIB/Smokey) using his body to escape the island and go "across the sea". Ben needed to be the protector, so he followed him and that is why he hung him. It was not necessarily an evil act, but was necessary to protect the island and the world. Then he had to make sure Locke's body, containing smokey/MIB was returned back to the island.