Like I said, I think the sound stage itself is a greater threat than any fan films produced there, because the original content doesn't serve to reinforce the franchise. For instance, one could make the argument that a good Enterprise fan film probably makes people more interested in Enterprise, whereas now independent series Renegades doesn't really do this.
I would agree if not for two points. First, cutting the run length to 15 minutes makes it impossible to tell the type of story that a Star Trek episode or movie tells because of time constraints, or to tell a story arch due to the series prohibition. Second, they don't provide any license or covenant not to sue, so film makers don't really have any form of legal protection no matter how friendly and respectful they are to CBS or Paramount. Either of these would go a long way to making me think it's balanced.
I too question the whole idea as a profit-making business model. As for something akin to a non-profit sound stage, I'm cautiously optimistic.