I had the issue with Slackjaw attacking me. I just reloaded and he didn't attack me that time. To be fair, I did poison his well and kill a bunch of his dudes in the art dealer's apartment. Anyway the second time worked fine.
Regarding non-lethal methods. In most cases non-lethal methods will present themselves to you in eavesdropping or being approached by a character.
For the first guy, I've done it a number of ways. Usually I just sleep dart them both and take them out the window so they can't be found.