Henry Hill seemed to be too small time to bother killing. I think his ties to Paul Vario were played up by him and Pileggi to build up his story. He must have known him, and they took a photo together once, but I believe Burke may have been closer to Vario. If they won't kill a Gravano or a Michael Franzese, they will not bother with a small timer like Henry Hill.
Actually in Hill's book he describes growing up very close to the Varios. He says he stood as best man at more than one of Vario's sons' weddings. The scene in the movie where Hill first meets his wife was true except he was actually playing wingman for one of Vario's sons. In Al D'Arco's book Mob Boss, D'Arco says that one of the reasons Hill got away with so much is because Vario liked him so much. So I think they were extremely close on a personal level.
The keyword being, "growing" up. This was nearly two decades later at that point in time. Hill was no longer a teenager and 20 something growing up with Vario's sons within the same age range. They were now grown men with children and families and while yes, they largely ran around with Henry and that Burke/Vario crew of hard drinking partiers, Hill was the extreme case as a legitimate drug addict and full time narcotics trafficker.
If you're going to cite his book, that's fair and I agree with your statements that he was initially very close with Petey and Babe Vario and Lenny I believe as well, however, in that same book it illustrates a very clear depiction of Hill all but totally recoiled from mafia live, living as a lower tier debatably mid level cocaine dealer in the suburbs of Long Island. He has no other action on the street but drugs at this time and is devoted to getting drugs to Pittsburgh and Atlanta, not running with Jimmy or doing scores for the crew. Food for thought, do you think Henry was really kicking up regularly at this point? I'm not saying he needed to or was expected to given his close friendship with his Capo's. That being said, my point is, out of sight, out of mind. Henry was left to do his thing at this point.
