A.S.
Don't let yourself be frightened. Do REAL research. I am constantly hearing that vaccines are the cause of autism, but when I actually look into it, pretty much all of the evidence I find is anecdotal. People thought that it was due to the thimerosal in the vaccines, but now they've taken out the thimerosal (even though there wasn't real evidence that it was dangerous) and it doesn't seem to have made a difference in people's opinions.
IMO you're better off protecting your kids from known diseases than making decisions about their health based on essentially random internet polls or secondhand stories. Make sure you have a family doctor, a real MD, that you trust and talk to him or her about it.
Probably the biggest reason why there are so many more kids being diagnosed with autism these days is that far more people RECOGNIZE autism in various forms. A child doesn't have to be Rain Man to be considered autistic anymore.
Feel free to try homeopathic medicine, but I wouldn't replace a regular doctor with it. It may make you feel better, but it isn't real science. Again, see a family MD that you trust and have a serious discussion about your concerns.
Good luck!