While I don't know exactly how it will work in NWN 2, the way I see it currently is like this:
The half-giant (since that is the example used) is much stronger than the other races. Sure, they have some drawbacks from their Int and Cha, but their other abilities more than make up for that. And on top of that, the majority of half-giants are going to be fighters or barbarians anyway, so they don't really need the Int or Cha that they have been penalized of. Thus, a level 1 half-giant fighter ends up far more powerful than a level 1 any other fighter. That is what brings in the ECL.
The ECL makes it so the character won't level up as quickly by configuring them to be, essentially, a higher level character. This is because they are more powerful and have more of an ability to gain xp quicker. Basically, the way I see it is that the ECL is just another way of balancing the character.
So, in my own opinion, I don't think the fact that you have an ECL should be taken into account for applying for a WL position, since its only real purpose is to balance an otherwise over-powered creature.