As the person who has been working on this, I think that a couple of important things have been missed.
Mission points are much lower than Raiding Points
... like, much much lower. I think that Con said that PvP points were about 5 times, but in actual fact I think it is closer to 20 times. The easiest mission areas are about 1/20th of what the lowest PvP level would be. In fact, with the rewards being scaled up, I think the Mission points could actually be too low at the moment, but we will wait and see.
Your missions areas are capped
I can't remember the exact number, but I believe that you valid missions are limited to about 5 levels below your player level. So as you level up, you can't just farm the lower levels.
The mission points are linked to your level
To counter the fact that higher level areas are larger, harder and have longer return times, the points for areas increase with the level. They are still substantially lower than the PvP points.
The White Flag is in effect
That means, if you put on a white flag, you can't get points. I'm sure there will be mixed feeling about this one, but we thought this was the fairest thing.
The raid points system should ensure that non raiders aren't at the top of anyone's target list, but it will also mean that they aren't immune to attacks either. You may not want to raid, but you will probably still want to defend your compound a bit.
The stats have been recording for about a year
This probably isn't as important as the other things, but I thought you might like to know that I have been recording your alliance pvp stats for about 12 months, so all you awesome raiders out there will have something to show off from day one.
Finally, and most importantly, all of this is fluid.
Nothing is set in stone.
We have taken our best guess at what we think is the right balance, but I am sure that it will have to be adjusted. We will just want to see the data before we do.