How rude of people to just say that you "didn't think it through." Sometimes life just works out a certain way and LOOKING BACK you can see your mistakes but at the time you couldn't. I'm sure everyone has something they look back on and maybe wished they had "thought it through." You didn't ask for their opinion on whether you "should have done something different" and the situation is what it is and you can't change that!
It sounds like you might be like me–originally thinking that you'd raise your children like typical Americans and then learning more and deciding you don't want to vaccinate and are avoiding some of the bad foods out there. Also, the Waldorf method is wonderful and it's great you took the time to discover it and learn about it.
Sounds like you might try to find some support before you break up the relationship. What I mean, is find some families out there just like you who think like you and have kids your son's age. I would never have been able to pull of some of the "strange" ideas I now have about parenting if it weren't for the support of other people who think like I do. Plus it will be support for your son to see other kids just like him.
My SD lives in two worlds, poor thing. At our house it's about healthy foods, limited TV, lots of art and exploring, no junk food, not much sugar, recycling etc. At her mom's it's about constant TV, junk food, late nights, rated R movies, etc. And she prefers our house! She even made her mom buy her organic snacks LOL!
I think you need a good conversation with your BF. I'm sure there are things you can compromise on. You'll have to grant his children the right to do some of the things you don't approve of for your son--but the funny thing is if you do that but continue to do things with your son a certain way they may change their minds on their own.
I believe in your house there are some things that your BF should compromise on. For example, your house, your bedtime rules. Your house, your food that you buy. Can you stop them from watching a lot of unimaginative TV? Probably not. Can you take it one step at a time? Get your BF to agree to ONE thing. Maybe a solid bedtime. Start there.
And tread lightly. There were some things that I noticed about my DH that he was sensitive about with his daughter and I had to phrase things a certain way. He thinks she is just so amazing and anyone who doesn't like her--THEY have the problem. So when we'd get bad reports from teachers it was always the TEACHER who had the problem. I have to phrase things a certain way so he doesn't blow up because I know that my SD has issues paying attention and following directions. I also just had to let him see it for himself.
Good luck! Your situation is not doomed, but you're going to have to take control, compromise and tread lightly. No one likes to think that they are a bad parent.