It would be passing weird if a federally-approved 501(c)(3) charity were told to stop operating on grounds that the very charitable purpose for which it was created violated federal law.
501(c)(3) status is not a defense against copyright infringement. Also, for reference, here's STC's mission statement as a charity: http://startrekcontinues.com/nonprofit.html
Anyways, as a huge STC fan I have my fingers crossed (a) that CBS doesn't care that much about TOS tribute films and will leave them alone, (b) that CBS will let STC go ahead with whatever money STC gets from this Indiegogo (though I expect CBS will put the kibosh on all crowdfunding by anyone until the Axanar case concludes), and (c) that after the Axanar case concludes, CBS doesn't kill off crowdfunding altogether but instead unofficially imposes per-campaign limits on the various fan film productions.