Vic Mignogna is working on a CBS licensed project though (Star Trek Online) as a voice actor. For the purposes of the guidelines, it doesn't really make much difference. And he continued filming and producing additional episodes after the guidelines dropped. Read that as you may.
To answer your question, no I likely wouldn't continue making fanfilms were I in James' position (thank you for the compliment by the way). Nor am I suggesting James should. My singular point is that the guidelines themselves do not preclude anyone (licensee or not) from making fanfilms. The guidelines simply suggest that such people working on fanfilms will mean those productions will not be protected by the safe harbour implied by said guidelines.
That doesn't mean that individuals may not be able to negotiate something (there's certainly plenty of speculation that Star Trek Continues may have).
Again, I'm not suggesting what James can or should do. Only he knows the terms of his deal with the studio, and it may be they have simply told him not to finish the outstanding episodes. We simply don't know. My point, again, is simply that I do not believe the guidelines alone are the reason for people to stop producing.
Indeed, and we know they wrapped early because of the guidelines. However, as stated above, they did continue to film and produced episodes after the guidelines landed, which didn't seem to preclude Vic working on Star Trek Online.
Have the guidelines made people step back? Yes. But there is nothing legally binding there, and I don't think it benefits any of us when people read more into them than there actually is.
Look, I realise I'm not putting this across well, but essentially what I'm suggesting is that the guidelines themselves are not binding. That said, I also think those who flout them do so at their own risk. And honestly, at the very least, I believe we should respect the wishes of the studio.