The reason this issue is such a problem and has naturally become a major stink isn't that Cryptic is a money-hungry monster, it's that the ship tier levels were poorly conceived and designed to begin with. Even if the new ships that are headed to the C-Store were diverted and worked into the tier system as it stands, there are still too many other current playable ships that already seem out of place.
The "Iconic" ships not included in STO thus far were either promised before launch or were reasonably expected to and should have been in the game to begin with. Let's face it, the "Iconic" content, no matter what it is, is what makes Star Trek "Star Trek". The addition of these vessels directly into the current tier system would shine too bright a spotlight onto this problem which unfortunately has no easy patch or fix. The only real solution would be to redesign the tier system as a whole, server reset, and reboot the game, causing an unknown number of subscribers to start all over again. I'm willing to wager that would not be a popular idea for most as many have already invested a lot into STO.
Adding these ships to the C-Store is an easy band-aid that is still something of a win/win for both Cryptic and it's subscribers. The players have the opportunity to get content they deem as crucial to the game/immersion and Cryptic gets to make a song and dance out of delivering it. Cryptic has every right to make money off the game; I don't know of one mmorpg worth it's salt that doesn't.
Personally, I'd rather see the whole tier system redesigned with ships in their appropriate places and a reboot to follow. My feeling is that STO should be "STO". I don't know of one single subscriber that subscribed to STO because they really just had a hankering to fly around in starships designed by Cryptic Studios. No, they subscribed because they expected to be able to fly starships seen on the tube and screen that they had come to love. Leave all the ships with futuristic, non-canon, loopy designs as C-Store fodder.