rsync could have a WIMP GUI and a console one. One does not preclude the other. I think you are right that embedding rsync in a more narrowly focused app might be the best option but it is not the only way.
And though I tend to be a GUI hater, Unison is one tool where I find the GUI much more useful than the command line alone. The game is to iteratively come up with a set of rules which Unison will use to into effect on your dataset. The GUI quickly show you the effect of your current rules, and lets you propose the next iteration etc.
rsync is a tool to copy data - it can keep two folder structures in sync but that is not its sole purpose.
Unison https://www.cis.upenn.edu/~bcpierce/unison/ is a tool to keep two folder structures in sync - that is its main goal but it can have other uses.
Unison happens to have a WIMP style GUI.
rsync could have a WIMP GUI and a console one. One does not preclude the other. I think you are right that embedding rsync in a more narrowly focused app might be the best option but it is not the only way.