Well, there is a lot of whining and complaining on the forum about it. I think it is partially justfied and partially not. In the end, I think Cryptic needs to look at how it can better communicate its programs without always ending up with a terrible uproar afterwards. This is meant to be constructive feedback.
1) Contine with Promotions and Referral Programs.
They are inevitable, and I say they are good for the game. They draw in new players. That's good for all of us. We want them.
2) Make the default assumption that _everything_ will end up in C-Store.
If you don't, there will be always complaining that items are not available for everyone and you just reward people with more money. And if things that were labeled exclusive, unique, special or similar terms are made available, people will complain about.
3) While _everything_ will go there, clarify when.
I suggest a default "wait time" of about 6 months. Half a year is a lot of time in the world of MMOs.
4) Consider to "upgrade" exclusives once items go into the C-Store.
The example of the 50 $ C-Store reward for Master Recruiters now is one way, though I think it's a little boring. An alternative would be to simply give these people access to another item that is still exclusive. Either at the same time then people participating in the promotion program for that exclusive, or a little later (1-2 months at best).
5) Special In-Game Titles, Ribbons that remain exclusive
This is the only thing you should never give out in the C-Store. Special items - like unique combadges, ear-rings, trophies and special titles should be tied to every exclusive. Be careful with these - they really need to be minor. Something unique like full clothing or races is out of the question, it must be something mostly decorative, otherwise people will demand it for C-Store anyway. It should _not_ be "canon" things, like say an alternative future combadge. This is stuff that every Startrek fan will find at least somewhat desirable and feel taken away from when he doesn't have a chance to access it.
These items are primarly for bragging rights. Everyone can get the Galaxy X, but only few were on Tribble playing with the devs that one night - and now they have that Dev-Hologram Trophy in their trophy room.