I couldn't find any evidence of synthesized vitamin D - AFAIK our vitamin D intake consists mainly of the isolated vitamin or fortified food. And looking at the structure of isoamyl acetate (banana oil), I don't think a stereoisomer is possible. Any structural isomers wouldn't be called banana oil. My basic point is that a lot of "non-organic" products are being passed off as unhealthy without any scientific evidence. The principal consequence is that some (expensive) foods become unfairly attractive to the clueless consumer. This could all be occurring in my mind though . It's good that you're wary of what you eat though, I don't think I could say the same.
You could be right, I don't know much about chemistry stuff. Or maybe it's a big conspiracy. Both good!
I think the important part about organic food is that it is [supposed to be] grown and processed in stricter ways. Of course, depending on who classifies it as organic and what the company itself is like, it's hard to say. A lot of "organic food" companies are owned by the big corporations, so you're likely getting the borderline "we can just barely call this organic" stuff.
What it comes down to is reading labels and researching companies. When possible, I buy from small/local companies that get their food straight from local farms. You're getting the freshest food that way, and you're supporting the local economy, too.
But yeah, I try to avoid artificial (and any non-identified) flavour/colour in food, because I hate the idea of eating something that I can't possibly research. At least when I see, say, "concentrated pear juice" on a label, I know what I'm getting.