[Brightcolours]

For the intend and purposes of the OP, quoted here "The goal is to automatically take pictures, do some image processing and then upload the results to a FTP site.", my suggestion fits the bill well.
He didn't talk about IQ. In term of programming the RPI solution is great, along the various tutorials. I this sense, I find it much more flexible.

"simple webcam or hd-webcam because the image quality of still frames isn't very good" that part makes it a bit less of a good fit, though.
The RPI solution is geeky, perhaps not great. No experience with the Canon SDK, but my impression is that it probably is way more "flexible". The shitty quality you can,t change as it has a fixed lens.