This may be a strech but what if there are two smoke monsters? One of them is the judge and one of them is the executioner.
For example, in The Cost of Living, after "Yemi" judges Eko in the clearing with the flowers he leaves. Eko follows him and is killed by one of the Monsters. If there was only one Monster why didn't he just kill Eko in the field?
And in Walkabout, Locke sees the Judge Monster, which is why it doesn't attack him. However, in Exodus Part 2 they see the Execution Monster which is why it attacks them.
I think that the two monsters may work together when they have to determine whether or not someone deserves to live, like with Eko. When not "on assignment" they roam the island, which is why some people get attacked without being judged, like in Pilot Part 1.
The Judge serves Jacob, whereas the Executioner serves his nemesis.