What I'm saying is: Seagull, because of the tight relationship, offers so much more than any regular bookstore would. Just by being a Covenant book in a Seagull store, you're practically guaranteed four or five thousand sales. If Seagull acted more like a regular store, not a Covenant outlet, that number would probably drop by half, if not more.
To trade those semi-guaranteed sales, due to the relationship, in exchange for getting listed in places like Amazon seems silly. For example, both of my books have been listed with Barnes and Noble since they came out, and at most I sell two or three books a month through them.
Granted, there are oodles of negatives that arise from the fact the Seagull pushes Covenant almost exclusively, and Deseret Book pushes DB almost exclusively, but in this particular instance, the benefit of wider marketing doesn't outweigh the loss.
(Really though, it does seem silly that Seagull would put such stipulations on Covenant's marketing. As few sales as my Barnes and Noble listing generate, or even my Amazon listing, it can't affect Seagullbook.com).