Hmmm ...
The ideal solution would be to offer the Multiplayer Exp. Pack (with a few other features designed to improve the quality of
both Single Player Mode and Multiplayer Mode, like the ability to automatically upgrade outdated ships) alongside the original version. That should solve the problem because (although you have probably already considered this):
1.) The people who didn't buy it because it lacked multiplayer might be tempted to rethink their decision it if they see the Exp. Pack for Multiplayer right next to it.
2.) Those who don't want Multiplayer but are still interested in the game can still buy it.
3.) The people who already have the game can buy multiplayer if they wish but aren't obligated (it would obviously have to be available online as well).
4.) Subsequent expansion packs can be released online (and save shelf space) to those who already have the game and to who it would most appeal.
5.) After you have are finished with the game, you could offer an eventual Gold Edition that contained the original, all the expansion packs, and one or two extra features (a strategy guide, or more ship jewelry, for instance).
My suggestion (although once again, I'm sure you have considered this) is to stop selling the Collector' Edition and replace it with the Multiplayer Expansion Pack. Its a 'Collector's Ediion', after all; that implies there is a limited supply.

I am relatively sure they still stock it in stores, given that I bought my game only a few weeks ago and it was the Collector's Edition (for the same price, too

). A better idea, perhaps, would be to take out the original version when you release the expansion pack and simply offer a Gold Edition (though with the option to buy the multiplayer pack seperately online if you already have the game).
But my point is that you might be able to lure more customers into the game by selling the Multiplayer Exp. Pack alongside the game, difficult though it might be. I already posted my list of ideal features somewhere above /|\