For those of you who have ereaders other than the Kindle/kindle software,
epub and other versions of Allegiance are now available from Crossroads Press, Fandemonium's ebook partner. I've had very good experiences with their customer service (they emailed me a link to download the corrected version of a book I'd bought from them before I'd even reached the flawed page, and threw in a discount coupon as an apology!) so if you have any questions, I'm sure the staff will be willing and able to answer them.
ETA: Also, I've heard from a couple of folks that their Barnes & Noble has shelved Allegiance not with the other SGA novels in tie-ins, but in regular SF under my name. I have no explanation, but it's another place to check for paper copies....