Agreed, it should be cheaper directly from the maker themselves, but the point above is valid, they'd like to unload extra copies they've got sitting around. Remember they didn't pay $39 for each of those boxes, so chances are they're still making a profit, just not as much.
I am one of those people who started off with an "improperly obtained" copies and had a blast with it, and was also very surprised by how Stardock conducted themselves with relation to copy control and DRM so I wanted to support them.
Didn't want to pay $40 for it, but I told myself that as soon as I could get it for $30 I'd buy it. I've never seen it that low, but I had a coupon for stardock directly so I purchsed it online for $29.96 exactly. Was very happy and am just waiting for the Entrenchment add on pack.
I think it would be great if we could in the future purchase just a CD-Key from the makers of software so that if a friend is interested in getting a game after seeing it, it's just a copied disc and a extra low price for a key. Probably a pipe dream....