Basically, my point is that the "running the source code" part is where all of the interesting stuff actually happens, and that's where the "choice" would actually happen.

It may be true that the agent "runs the source code and outputs the resulting output", but in saying that I've neglected all of the cool stuff that happens when the source code actually gets run (e.g. comparing different options, etc.). In order to establish that source code A leads to output B you would need to talk about how source code A leads to output B, and that's the interesting part! That's the part that I associate with the notion of "choice".

This may help you. (Well, at least it helped me -- YMMV.)