According to this story over at WarCry, this is indeed the case. Perpetual, now known as P2 Entertainment, appears to have handed the project over to another developer. WarCry says that this news has been verified by a number of sources. Sadly, there's no info yet as to who exactly has taken on the project, and the reasons as to why P2 has decided to drop it.
In days gone by, I was a pretty hardcore Star Trek geek. I even had my picture Photoshopped into the Original Series deck with Kirk, Spock and the rest of the crew when I was around 15. So the idea of a Star Trek MMO has always interested me. Unfortunately, when you hear this kind of news, it makes it hard to see a happy, successful future for the game.
P2 Out As Star Trek Online Developer [WarCry]