I did a lot of experimentation with this as well. When I first learned OpenGL I also wanted pixel for pixel relationships between the graphics I create in photoshop and my placement of those on the screen. For some games you will want exactly that. I'm not classically trained in OpenGL. Instead I taught myself. So I don't know if it's normal or kosher or whatever. And I guess I don't care.
But because all OpenGL variable have a precision hint, it's actually better not to use the actual pixel values. Instead use math. Also, keep in mind that at least for another year or so we might want to support non-retina devices. So those don't have the same number of pixels. But you don't want your game to have to be coded for multiple screen resolutions. And OpenGL can do a very decent job of resizing your graphics, although it does come at a speed price.
My suggestion is to pick a scale factor for your units. 1 unit = 10 pixels or 1 unit = 100 pixels. In my games, I've chosen 1 unit = 20 retina pixels at a specific depth.
Another tip.. don't do orthographic. Go ahead and do a perspective view. Why? This will give you the opportunity to move things in Z space if/when you want to. You're just going to place your objects at a z depth that has pixel for pixel "unity" (not to be confused with the 3d game engine).
If you do use ortho though you can use this frustum:
int frustumScale = 400;
if (retina) {
frustumScale = 800;
}
matrixFrustum(-(float)backingWidth/frustumScale,(float)backingWidth/frustumScale,
-(float)backingHeight/frustumScale, (float)backingHeight/frustumScale, 40, 1000, frustProjection);
Where frustumScale is 800 for a retina screen and 400 for a non-retina screen. Then at a distance of 800 from camera (-800) the sprite is pixel for pixel the same as photoshop.
Check out this question and my answer here: In 3D camera math, calculate what Z depth is pixel unity for a given FOV
Note.. I don't use glKit. I didn't want to learn an apple specific way of doing OpenGL. Instead I wrote my own math library and engine. But the basics are probably the same in glKit.