I honestly don't know why this isn't done. Nearly every time there is an update something gets buffed or nerfed for PvP or PvE that negatively impacts the other, and many times is an uncalled for change.
As a quick example many people would know....the huge round of changes that nearly destroyed concealment Operatives in PvP, because of PvP, severely impacted the same tree in PvE, mostly ridiculous changes that made no sense if one did not PvP.
Jarring strikes 3 second knockdown was ridiculous in PvP, to be sure, but was a highly useful ability for the leveling Agent.
And honestly increasing backstabs cooldown to 12 seconds did absolutely nothing for PvP, but hurt PvE Operatives for no reason other than for the sake of PvP balance..
A more recent change being inquisitors Overload ability, and all similar abilities, being changed from a circular knockback to a cone knockback.
TL;DR : Separate skills for PvP and PvE and balance each game separately.