A switch sounds good to me. For me, the junctions are a great improvement on Windows. But yes, I think the “normal user” is not able to setup ignores when he first tries out Syncthing coming from somewhere else and still needs to discover and learn.
In my opinion “default ignores” would be a nicer approach because we know that it’s mainly %userprofile%\KnownSystemJunctionFolder causing the cosmetic problem. If we could detect “user creates a new folder with %userprofile% as root” we could then ship those ignores.
Update: Not a good idea as Microsoft made those folder names localized 
So instead of filtering for the folder path on creation and auto-turning the junction follow off a default to off would be better. It could also be called “junction strategy: ignore” on the UI (like Duplicati has it).