How stable are node and edge IDs and their ordering? Could you sort the JSON before saving so the output is more stable and diff-able?
Another thought is, how would you code up a flow like this in your preferred language if you were just writing code in that language (you didn't care about the visual editting). Call most of the same functions, but do it directly. Ok, think about that, then write a transformation from the NODE language to output source in your preferred language.
I have some sense that coding this type of control flow logic doesn't work well with text line based diffs because of the complexity of the problem, less the syntax.