Its going to be an interesting fourth season that's for sure.
I think Connor perhaps will be a little on the dark side, i mean, with Justine beside him, what would you expect?.. Perhaps Connor will realise the truth about his foster father's death and Justine's role in it, maybe be guilt-stricken and perhaps employ Wes (how i don't know), Fred and Gunn to get him back...
I don't think Angel would/could kill him.. I don't think he would trust him, but his one chance of fatherhood, i think, despite everything that happened in the season three finale, that's still precious to him. He told him that he would always love him whilst they were strapping him in.
Those are just my thoughts, and i can't wait til the first episode of the fourth season airs, so i can find out how Angel gets out.