I'm not so sure the taped conversation with Ed happened as part of Davids death. Why kill David but not Ed? Especially if they thought that Ed knew as much as David did. I'm thinking the conversation was earlier, and the interruption is not really a dangerous moment. It's just him being interrupted, and not wanting to continue talking in front of whoever came in. David appears to have been at home the night before the accident. His Wife doesn't say anything about him not being at home or anything seeming out of the ordinary with him. I would have to go back and watch the first episode again, but isn't David talking to Will on the phone from the train that morning? Atlas kills people who compromise them. If they thought Ed knew too much then they would surely deal with him. as well? Truxton will find out sooner or later that Kale has been helping Will. The Atlas guys not checking in with an update on Will, is going to be a HUGE red flag. The **** has hit the fan! It will be interesting to see how they are going to lay out the board for the remainder of the game. You could just see Will thinking back to the party at Truxtons house when Kale told him to stick to the analyst side of things, because he would hate to see him involved in any mayhem.
Ed is a barely functioning nutjob. I'm pretty sure they don't think of him as a threat. David, on the other hand, was a problem. As for Kale, I think Truxton already knows about his helping Will. That's why he's getting bugged and tailed. I also don't believe that "best interest of the US" bullshit.