The problem with vitalism is that it's unfalsifiable; that doesn't mean that it's wrong, simply that science doesn't have the ability to refute it.
So your analogy really should be between lab-synthesized vitamin C and a piece of citrus fruit. The fruit is going to be better for your overall health because it's got more in it than just L-ascorbic acid. For example, it's got fiber, which is likely to slow down the passage of the vitamin through your digestive system, which will help you absorb more of it for an equal dose.
Joe Public> I have a headache.
Folk Medicine Dr> Here, drink some willowbark tea.
DrugCo Chemist> No, take this aspirin. It's chemically identical to the active substance in willowbark tea, but much more convenient!
Joe Public> My headache is better, but now my stomach hurts. That never happened with the tea.
DrugCo Chemist> Oh, you have an ulcer. You're a sick person. Take this antacid medicine!
Joe Public> My stomach feels better, but now I'm constipated.
DrugCo Chemist> Wow, you're really sick... here, take this laxative!
Folk Medicine Dr> All these unnatural drugs are killing you. You should really just take the tea.
Joe Public> Yeah, I think you're right. Natural is better.
Also, you're the one talking about magical vital properties, not me. It's a well-established fact that substances in combination can have a different overall effect than they do in isolation. There's nothing magical about it.
Homeopathy is an absolute scam. And yes, there are scammers who take advantage of the 'natural is better' idea to sell useless products.
[1] https://en.wikipedia.org/wiki/Vitalism