Savin, have you ever played Eve Online? The structure of this game more closely resembles that than any other game. And, it's not a gankfest, but there is some ganking that happens. With some tweaks they could easily shift the balance of secured area PVE vs PVP that would more favor the PVEers.
PVP can be effectively done in PVE areas without it being a gankfest. Yes, it will cause the Devs to have to be proactive in managing their product but, if they aren't proactive in ALL areas of the game then it will be broken anyway. Eve has experienced hundreds of exploits that cover everything from macro mining, pvp, the market, pve and everything else. Exploits aren't unique to greifers and, greifers aren't unique to pvp. If the Devs are unable to proactively manage the game then its doomed to failure anyway as plenty of non-PvP exploits will be found and need to be patched up.
The problem I see with this artificial wall between PVP and PVE is that it is extremely restrictive on the sandbox nature of the game. It closes all kinds of opportunities for building your own playstyle that is the attraction of sandbox style games in the first place.
In its current form you have very limited options on what you can do as a "career" in game. Mine, harvest, build stuff, PVP, or farm NPCs. Those paths don't vary much in their application due to strict rules in place regarding player interaction. The whole point of the sandbox style game is to have fairly loose rules that intelligent players can exploit to improve themselves.
Those exploitations can generally be measured by risk taking. The more risk you take and the more creative your approach, the better you do. In its current form you can either farm Alpha islands with almost zero risk or go full on combat PVP. There isn't much of an in between, no shades of gray.
I prefer industry over combat but, I'm bored senseless if the only form of risk comes in the form of some kind of random NPC that might cross my path while mining. Or, I can try to hop onto Beta to attempt to mine and be insta-ganked within seconds of teleporting.
With the majority of the population sitting on Alpha islands with little risk and the rest being mostly self sufficient on Beta Islands there wont be a market to speak of. I'm limited to nothing but the constant grind of mine, harvest, build, sell (if I can actually find a buyer).
PVE content will never create enough material turn over to support any sort of market system that would be a viable career choice. The Perpetuum market will more resemble that of WoW than a full on sandbox MMO. PVE players for the most part know what content will cause them to lose their gear and avoid that until they've done the grind to build the equipment they need to be able to handle it. The only option that I can see is Bind on Equip or Bind on Pick Up items like World of Warcraft. I think everybody in this forum would agree that WoW is not a good direction to send this game. Besides, there's a new Star Wars MMO coming out if people want WoW in space.
That wall between PVP and PVE is really only suitable to linear style MMOs like WoW. IMHO it will break a sandbox style game at some point. And, the less active the market the sooner it will break.
It's not a zero sum game as far as open pvp goes. PvP elements can be mixed into 'secured' parts of the game without the greifer types dominating it. You just have to build game mechanics that fall somewhere on the scale in between the gankfest games and Farmville.
And the PvP flag system is silly on Alpha islands. Flagging would be the equivalent of a self destruct button.