this is a long time ago question with no answer, but maybe someone has a solution now.
I'm having the same problem.
If I use mp4 format in my Sony Alpha-65 instead of AVCHD, it creates mp4 videos with 1440*1080 pixel and 16:9 aspect ratio, with 25 fps, AVC (Main@L4.0).
These are 16:9 videos and displayed with 1920*1080 pixel in all applications including Quicktime, Aperture, etc.
Just if I use this video in a diashow in Aperture it is compressed and uses a 1440*1080 format with something like a 4:3 aspect ratio..
As this only appears in Aperture diashows, it seams to be a problem there.