I'll admit that I know little to nothing about Steam, but it sounds like Steam purchases licenses from SE under some type of business-to-business agreement with SE and "resells" them to you, the end-gamer, at a discount under their own umbrella? If that is the case, it seems to me your issue might be with Steam/Valve, not Square Enix. Since you paid Steam for the license and agreed to have that license managed through Steam, whatever software purchase agreement/contract you have is with them, not SE (which is different from the end-user agreement you agree to through logging in and playing the game). Therefore, any licensing issues - such as not being able to register a steam-free version of the game key on PC - would be a Steam issue to handle as your "licensing provider".

If any of the above is remotely accurate, I can pretty much tell you right now that what you are asking for is a pipe dream. Steam is never going to give up their FFXIV revenue stream without a considerable fight - a fight that I highly doubt SE will get into the ring on (assuming they even could depending on their B2B agreement). Square Enix isn't going to jeopardize what I am sure is 100s of thousands of licensing dollars from Steam (money I'm sure they get regardless of if Steam sells the license) for this kind of issue.