There is exactly one thing you have to understand about the new Star Trek fan film guidelines. They are a promise, not a threat.
The promise is actually pretty impressive. Not quite unprecedented--Lucasfilm embraced the fan film community, albeit with a few reservations--but this is a pretty big deal. Paramount is saying that they will let anyone, for free, make their very own short film based on one of the four biggest entertainment properties in science-fiction (Marvel, Star Wars and Who being the other three), for free, gratis, so long as certain rules are adhered to. Are those rules pretty stringent? Sure. Do they let you make your very own Star Trek with absolutely no threat of legal action by the holders of the IP? Sure.
And if you don't want to adhere to those guidelines...you don't have to. Sure, you could be sued by Paramount, but what people are forgetting in their initial judgment of the new policy is that this was always the case. All Trek fan films prior to this point, every single one of them from the officially unofficial series that used Trek actors playing their copyrighted characters down to the guys wandering around in their heavily wooded backyards in pajamas yelling, "I AM KIROK!"...they all risked a lawsuit. Because they were infringing on someone's intellectual property. They had no legal defense against that, none of them. It wasn't fair use, it didn't matter that they weren't making a profit, it didn't matter how it was distributed. They all were potential targets.
So nothing has changed for these people. Officially, 'Star Trek: New Voyages' is operating outside the guidelines and is vulnerable to a lawsuit should Paramount decide to go after them. Officially, Paramount can't say to them, "Hey, we don't really care, you're not making any money and your show is good PR for us so knock yourself out." But that was the case yesterday too. All this is, when you boil it down, is a way for Paramount to cover their butts so that when someone like Alec Peters comes along and raises a million bucks to make a feature-length movie while selling bootleg merch, he can't say, "Well, I had no idea that I couldn't do it!"
Of course, that won't stop fans from freaking out about it, but hey. Fans gonna fan.