Browser-detection (and by extension, mobile-device-detection) is fairly trivial (though I admit I don't know offhand what a kindle-browser identifies as, but nor have I tried to download something direct to my kindle from a website – not sure if the browser necessarily connects to the file system like that). You could insert a small script that offers the appropriate format based on browser detection, and a clearly marked option for them to choose another format manually (including a zip bundle) in case your detection went screwy.

I'd couple that with a permanent sales history, so people can come back if they've changed devices and redownload.