I'd be worried about bending and deformation when trying to cap. You could try though and see what your results are.
Also, sanitizing will be an issue if you use Star San. Star San is an acidic solution and will take the aluminum oxide layer off the outside of the Al bottle and possibly render it reactive or able to solublize into your beer. This could possibly cause bad metal tastes in your beer. Also, its likely that bleach, a basic solution, will also remove the aluminum oxide layer. (Aluminum solubility is lowest at neutral pH (pH ~ 7), as are many metals). I'm not sure how you'd go about sanitizing aluminum bottles, though I guess you might think about baking them.
As a note, I've been using pop cans because they are very plentiful around my apartment due to my roommate's 3+ a day Diet Pepsi habit. When frozen with water and dropped into a half-strength solution of Star San as a water bath for cooling some interesting chemistry happens, with some sort of white precipitate forming on the cans and in the water.
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