How does the graphic look if it is purely scaled down in AE without any corner pinning? It is possible the issue is related to the render/filter quality of the AE scaling in general and not the corner pin?
If you'd like to post the files for me to look at, I could do tomorrow.
As far as "align surface" this feature is commonly used if you wanted to paint or clone some the image and than apply tracking to that. You don't want to scale down your paint to the surface, you want the surface to remain full frame. Or in your case, you position the the logo (insert) within your comp rather than scaling down to the tracked surface.
This is covered in a few tutorials such as:
http://www.imagineersystems.com/products/monet/Mocha_aftereffects_workflow....
or:
http://library.creativecow.net/articles/larsen_carl/simple25d_rig_removal/v...
Ross Shain
Imagineer Systems
www.imagineersystems.com
