I think there can be a balance; take the PvE ammo nerd that you mentioned, they have shown they did this on purpose in the patch notes, where it states they reduced the ammo crucible heavy ammo boxes give in addition to the machine gun nerf. To put it simply, the could just have changed the value of ammo given by ammo boxes in PvP and left PvP alone. In addition, the can change how much a perk effects a guardian in PvP as oppose to a minion of the darkness (they have done this before, the touch of malice being the best example). They can even change how much damage a weapon does in PvP alone. The question I cannot answer is why they nerf the PvE experience.