Hi Andrew;
I'm sorry that your sister was scared by what she found. It doesn't sound like the movie itself scared her so much as what she found when she went online and looked at the various 2012 sites, is that right?
As far as the movie goes, Emmerich has said in interviews that he started out wanting to tell a modern "Noah's Ark" story, and that his co-author on the screen-play suggested that they wrap the story in the whole "2012" thing. The movie is not about any of the "2012" scenarios that are suggested on most of the sites… instead it is based on a completely different, but equally nonsensical scenario… that solar neutrinos are somehow suddenly different, and begin heating up the core of the earth, causing the destruction portrayed in the movie.
The plot of the movie is really about the survival story, how the governments "knew" about it in advance, and planned to save the rich and famous, etc. The whole "2012" thing is really an afterthought in the plot. In fact, someone told me that the Mayans were mentioned only a couple of times, for a total of 30 seconds (out of a 2 hour 40 minute movie).
As far as the other stuff your sister has found online, the only advice I can give you is a) listen to her fears, b) validate her feelings ("I can see why you are scared") and c) discuss them with her, breaking down each thing that has her concerned and showing her why the 'scare sites' are wrong, and d) showing her that those sites are in it for money, selling books and videos, etc.
I am not a psychologist or psychiatrist, but I am a parent. I'd be happy to help your parents discuss this fear with your sister in any way I can. Please use the contact form found under the 'Contact/Comment' menu at the top of the site, under 'Contact Site Admin'. That sends an email to me. Feel free to use that if you need further help with your sister.