Those two pics of mine do not show very well the amount of rust through. On the front channel, the upper side is completely gone in places like yours, and the sheet metal going back is paper thin. I think those vinly tops must be like a big sponge, when they get wet they hold moisture across the whole roof. i tried brushing the surface rust also, and the metal is pittied very deep. If you don't get the rust out of those pitts, it will be back.
Good luck, hope this helps in your decision.