There is a concern right now that the no-PvP zones will be exploitable by people standing right by the border and switch sides as they please. This will not be possible because there will be a timer that will come in effect when you enter or leave the no-PvP zone. So if you are in the no-PvP zone, when you leave it you will get a notice that you are leaving it as well as a timer that will indicate the time until your protection wears off. Similarly, when you are entering the zone the timer will indicate in how many second your protection will be enabled. One extra small detail is the fact that the protection that will be applied to players in these areas prevents them both from delivering any damage to either players as well as be damaged by other players. Because of this, standing in the protected area and shooting at people outside it as well as the opposite is not possible.
As for the alignment system questions, killing other players will still make you go red. It's just that there is no game mechanic that reacts to this any more. No towers will shoot at you and there are no areas that are off limits. However, players can use the information as they see fit, it's totally up to them. Red players as well as everyone else, cannot be attacked in the no-PvP areas.
Also, to address the concern about people staying in the protected areas to farm materials with no risk, the nodes in those areas will not be dropping the same items as the rest of the world. The world is divided in areas that we internally call danger zones. The higher the danger level of an area, the better the chance for special and rare resources to drop. Of course, protected areas are set to the lowest setting, meaning they will be dropping next to no rare resources. Additionally we expect these areas to be quite populated because of their safety so the nodes in them will probably be empty most of the time.
Source: forums.darkfallonline.com/showthread.php?t=331878