And she is free to say it. It's the Secret Service's job to protect the President--whoever the President is--from threats. Part of that job is to investigate pretty much anything that could be construed as a threat against the President. The vast, vast majority of those investigations are closed without any action, or, at most, with a visit from a couple of Secret Service agents saying (in more polite, official terms), "Don't be an idiot." The fact that the Secret Service is investigating this does not mean that she is not "free to say" what she said.
Nor is the fact that Cold Stone fired her a restriction of her freedom. She is free to say what she said. Cold Stone is free to decide that they don't want to be associated with such things, and to fire her for saying it. Frankly, if I were in that position, I'd fire her too. At the very least, even if she did not intend what she wrote as a threat against the President, making such a statement publicly shows extremely poor judgment. Having an employee who is apt to demonstrate such poor judgment--especially an employee who deals with the public on a day-to-day basis--is a significant liability.
I think there's validity to what you say *if* she identified herself as being an employee of the company she worked for.If she's known on facebook by her first name and doesn't reveal where she works I think that dismissal might be unwarranted.