Well, there is a way that you can support your local independent bookseller and enjoy your e-reader guilt free.
Several independent bookstores allow you to register for the Kobo Store through them, so every e-book you purchase benefits your local bookstore.
But you have a Kindle? No problem, there is an amazing little program called Calibre that will convert ebooks from the Kobo format (EPUB) to the Kindle format (MOBI).
Happy reading!