Or perhaps the focus was never to be on those characters who appeared with the freighter. The story belonged to those who were on Oceanic 815. The exceptions were Desmond/Penny and Juliet because they lived with the survivors, interacted, and became part of the group.
I agree that there is where the focus was and, given how many characters entered the story at one point or another, it was narratively economical to limit the effects to the core 30 or so, with in-laws as appropriate.
And one other thing: those who appeared on the freighter, except Miles, were evil through and through. They would not have qualified to enter the church at the end.
One last weird thought: why not Jacob in the church at the end?