You make a good point. I guess things just start feeling less natural when they have undergone heavy processing.
But you know, just because something's a plant (in your example of marijuana), it does not automatically mean it's good for you, either. There's enough plants out there that can kill you when eaten!

To me, it's just about what's beneficial. As an example: sugar is bad, honey does basically the same thing. It'll make you fat when eating too much of it and there's the whole blood sugar thing. However, as opposed to processed sugar, atleat it has the aditional benefit of having some good properties aswell. So then it just becomes a thing of picking the lesser evil.