I've had this happen to me as well, in one case there were 3 zombies inside a locked shed, and i know because their arms were glitching through the walls and they were "chasing" me. Kinda funny, but definitely a bug.
you dont start with a pistol, but you can sneak into buildings (high value barns are nice) and find a hatchet or a shotgun usually and now youre set to go, I find that this map is quite helpful http://dayzdb.com/map
just a helpful tip, try not to spawn in on the loot spawns, otherwise youll have to get away from them to have them respawn, and thats some wasted time, happy hunting :)
Don't feel bad about killing someone, especially someone in melee range with a melee weapon, if he stayed at a distance and did a salute or something, making his presence clear, sure, but that guy definitely wanted blood and you acted correctly.