There has to be such little solvent in a 'Sharpie' mark around your rope as to be insignificant. Also, that nasty smell from the marker you scent as you use it? It's mostly the carrier solvent from the ink evaporating, which in theory at least,(should) minimize attack on the rope material by the solvent/ink-and even if it didn't a few milligrams of solvent or ink for that matter won't hurt a thing.
I really don't think a guy has much to worry about putting a mark that is a few microns thick, an inch long,around a 10mm diameter rope?