I don't think that would be a viable solution, as it would mean that buying a Collector's Edition nets you two digital CE keys for one, and nothing would really be stopping you from using the one you need and giving away/selling the other one.
That could result in some serious losses on Square's part. The ideal solution is just for Square to come out and either tell people who will be purchasing on Steam there is no viable way for them to buy a physical CE, or acknowledge the flub and pledge to offer Steam keys to people who buy the Physical CE who would need one, though you could argue in doing the latter you'd run into the same problem unless there was a way to void the physical CE's normal key. I guess it boils down to how much they care about customer satisfaction over potential lost revenue.
