Supposedly, and this is a rumor, not confirmed fact, the pre-order agreements were made by Atari with the individual retailers, meaning that Atari would have to participate in breaking off those agreements.
EDIT: again, supposedly this is why the liberated borg engineer isn't in the C-Store on tribble (among other things).
Under Atari managment, Cryptic probably could have gotten a pack to market with all the preorder goodies, but under PWI, that's much less likely, if any of this is actually true.
I hate to relay unconfirmed rumors, but, there you go.
If they can't sell the original versions, they could always make something similar. If F2P is going to be a success they'll be releasing a lot of packages, they may introduce the complete DS9 pack containing various weapons that only appeared on DS9 like the TR-116, a Bajorian phaser, the Dominion bladed weapon (can't remember the name) and a few other things like the type 10 shuttle from the Defiant.
That would open up so make other packages as well for Ent, TMP, TNG, VOY (if we must but i did like the type 9 aerodynamic shuttles)
But that's me thinking out load, and my flame suit is engaged just in case.