I would like to think that they wouldn't punish the whole fan film community because of Alec, but you can never be to sure with these kind of big corporations.I'm no longer surprised to run into people who grew up on TOS or TNG and never heard of Star Trek fan films.
Enjoy them while you can because nobody knows how far the lawyer in training pants will push CBS this time.
If a lawsuit obviously didn't stop him form profiting from CBS' IP. I'd hate to think of other tools CBS may have in their tool box.
I know he was kind of responsible for the fan film guidelines being released, but I think something like that was inevitable after things like New Voyages/Phase II, Continues Gods and Men, and Renegades, so it's not entirely on Alec. Now, on the other hand, if somethig he does leads to a crackdown on all fan films, it will be.