I don't think it would ruin the concept of 'war', it would certainly redefine it. Assuming that your enemy has found an Arkification token and made source invulnerable, they would still have to transport or move to the location of the conflict. You may not be able to destroy the base, but you can certainly destroy the line and attack them in transit. This could force the conflict to an area of your choosing instead of at your home.
I think the mentality of "Wolves" and "Sheep" is doesn't really help PVP and PVE community relations. It denotes a definitive predator vs prey mentality and while I think that it does accurately define how the some of the people in the communities feel about each other, it should be something we strive to move away from.
I believe that PVP and PVE is really a matter of Risk and Excitement. When I have played PVP there is a huge thrill involved in the hunting or fighting someone who is as skilled as you, and with that comes the high risk of loss. For me PVP or high excitement high risk game-play while fun occasionally, is not really worth the higher risk.
When I play in PVE, there is excitement in challenging the environment, and in other games it can be fun to fight large boss enemies and hordes of enemies that may be set to match your skill level, but there is less risk because these enemies operate on a set logic. Their strategies are limited. In other games being able to unleash your creativity and build amazing things is exciting.
I look at it like this: In Minecraft there are 2 main modes, survival and creative. On single player these are both PVE. Creative mode is really fun, the possibilities are endless.You can experiment with different designs and setups and its great, but after you've created something awesome in creative mode, it's fun and challenging to bring these creations into Survival mode. You can still build amazing things in survival mode, but now you need to stay alive so that you don't lose your resources. Now there is small risk, and that makes creating, to me, more rewarding and exciting.
I think the Virtual Building, Ark Safezone, Arkification zones, and Territories are a good idea and that we really don't need any more protection than that, these are all things that the Developers have said even though I personally prefer to have player built shields with varying degrees of effectiveness in stead of Arkification Zones. For PVE their will usually be some kind of risk. (with creative mode minecraft being the only exception I can think of.)