I can't figure out why Lock would let Miles stay with them....do they trust him more than they do the other people from the freighter?

I honestly thought Ben was going to put a bullet in his head after what happened to Alex.

I think he's alive for two reasons:

1. To stress the point that between Ben and Widmore, Ben is the lesser of two evils (e.g., he's not going to fly off the handle and put a bullet in Miles head just because he's angry).

2. His "special talents." Might this come in handy with Jacob? Surely Ben knows what he can do.

He could also help Ben talk to Alex.

Excellent point.