It doesn't effect your game. If you choose to disarm the megaton bomb after the sheriff is killed then you need to talk to Harden (Simm's son) to get your reward.
I always just straight up disarm the bomb first thing once i reach Megaton because I like having a house and I don't feel guilty later when I slaughter everyone in Tenpenny Tower (minus Herbert though because he's awesomeî)
When you tell Megaton sheriff that Burke will blow Megaton, Burke Kill the sheriff. Is that good or bad for me??
good for you because you the get his loot without the town turning on you. if you would want the sheriff to live, attack burke after you done talking to burke. the town won't turn on you.