In an interview with Eurogamer earlier today, Emmert addressed the issue head-on and allowed for a future where F2P STO happened. For now, the company is going to wait and see how Champions fares before making any decisions about STO's future: "We're not sold one way or the other with Star Trek yet. If people want Star Trek to go free-to-play then get in and play Champions and help make it a great success, because that would send a strong message. If we did Turbine's level of success that would certainly merit the discussion!"
However, Jack Emmert says the decision isn't his alone and refused to commit one way or the other. He does hint at a fourth project that Cryptic is working on, one which is not fantasy-based and is "close to my heart."
For speculation on what a free-to-play Star Trek Online might look like, make sure you read Ryan's column on the subject.