I played the Episode Missions before the Pilot aired. There was plenty of time to get on board and do just that. That being said, new players are going to be missing out on the prequel before the first episode airs but they will get to participate in any missions leading to 2nd TV episode and beyond.
It really should be seen as no different than missing a TV episode. During one of the Comic Con panels, the developers did mention they would bring the Mission Episodes back for people to play after the TV season ends. This is an experiment and to them it is important to see how many people will play the Episodes in a timely manner. This is because for Season 2, they would like to have the Game playing between episodes possibly effect minor things in the TV series on more interactive basis.




