If they'd implement using in-game earned starfleet merits or energy credits, marks, medals, badges, whatever to earn C-Store items as well as real money ...... I bet that would quell a huge amount of angst.
you should be able to grind/earn/whatever ALL of the c-store items if you choose to, or choose the instant gratification of buying them outright for cash....let the players decide what they would prefer...
Thats a workable mechanic, assuming that they set it up so that a decent number of people would still shell out cash.
This would likely involve making the acquisition in-game very difficult or time consuming, but this would suit me just fine as the harder it is to get something the more sense of accomplishment you have when you get it, especially if you got it for free because of all that work.
It would give people yet another thing to stick around and work towards.