Assuming that in a C(onflict) Z(one) you shoot at and/or destroy ships that belong to the minor faction 'A' which in turn has allegiance to the superpower 'Alpha', I think that gets you negative reputation to 'Alpha'.
Is there a point beyond which when you fly in the 'Alpha' space or in an 'Alpha' system anyone can shoot at and/or kill you legally?
or even worse, you end up as the target of an assassination mission given by a minor faction or even the superpower 'Alpha' itself?
I always try to go unnoticed and I don't like CZs and all that but I need to get 43 more combat bonds and it's hard to find where and with whom to fight for or against, when one faction is independent the other is 'Alpha' or 'Beta' etc.
Does it matter if the faction you fight for or against is a player faction or NPC, any pros and cons?