Computers work in square pixels, TV works in non square. QT Pro can convert on the fly if you change the movie info but you can't tag a Quick Time of AVI file with pixel aspect ratio information (stored in the file header) with any rendering system that does not allow you to pick the pixel aspect ratio in the render settings.
The work around is to work in Square Pixels. Bring your Non Square footage into AE but create a square pixel equivalent composition, work there, render there, and, especially if you're planning for web distribution, pick a standard frame size that's square pixels for your final render. This goes for HDV as well as PAL, NTSC and DV formats especially.
What Rick said.... Attempting to gauge the quality or even technical correctness of anamorphic content, for SD resolutions no less, is bound to fail by just watching it in a player software. Now there are smarter players than QT, but that doesn't really settle the problem, as their built-in aspect ratio correction is dependent on how it was coded, whether it uses graphics acceleration and whatnot. Likewise, additional interpolation may mess up fields and so on.... That may not matter for just viewing a DVD, but it matters if you're the one producing it. So the best you can do is watch your stuff via calibrated preview hardware or burn test DVDs. Otehr than that, as Rick also said, working with square pixels is preferrable up to a point - if you obey correct sizes, nesting comps to then produce anamorphic output will not be a problem and within the Adobe tools, all otehr programs will correctly recognice the square pixel stuff and convert it to anamorphic as well, if necessary.