They should be more concerned with the REST of the crap going on in this game (or most often, NOT going on) and less about which ships are being flown around by the players.
Honestly, the "CBS doesn't like the idea" line gets tossed out a lot by Cryptic, and it doesn't ring all that true to me. Weird that CBS is fine with a year-long content hiatus of a game that had only been out a year (thus hurting their product), Star Trek being all about killing people with not diplomacy or exploration, an openly hostile message board, etc.
But they don't want to see people flying around in the Enterprise.
NX-01 or even a Vulcan ring ship is fine, of course (-150 years from even TOS, so what, 275 years out of date as of STO story time?), but a Connie would be a show-stopper. Not even that they don't want it in the game, but CBS is actually worried about game mechanics, and which ships are more powerful at what levels?