Wild Tangent Inbound:
Hell, if you really wanted to emphasize a good risk-reward factor to characters fighting in the Wilderness against enemy shinobi, all you'd need to do would be increase the amount of exp they earn for their jutsu while participating in combat there. Sure, you could always take the long, safe route of training your entire life within the safety of the village boundaries...but having the option to roll the dice and gain massive boosts in the perma-death zones adds extra tension, a bit of a balance factor...and a really, REALLY good reason for there to be constant combat in the one place most players won't be particularly comfortable going into (making it far more difficult to just sneak through these areas, as encounter rates will be higher and more players will be aware of the lay-of-the-land).
It might even adjust some players to the fact that it's okay to *lose* characters forever...there's always another chance to build one even stronger the next time. On top of that, combat in the Wilderness would also emphasize teamwork and efficient combat strategies...to the point that the best players could probably be seen most often duking it out in these high-risk zones, fighting over scrolls, raiding Rogue Organization Hideouts and even chasing down enemy agents through the trees/hills/mists/dunes. I imagine many a Kakashi will be born of the encounters within these perma-death zones ^_^).