One could clean up, prep and paint touch up the now bare spots. Then, as maddog34 mentioned, use a cable housing or noodle liner that fits within the guides. Do know that depending on conditions these anti friction liners tend to be of limited lifespan.

If you do decide to touch up the paint consider how much opening the guide have to accept a liner over cable. If there's any burrs or filler closing up the openings now would be the time to deal with that.

I have run my gear cables bare against many of the frames I have built since the 1970s. Only the times I neglected their maintenance for too long (cleaning mostly) have I had issues with gear shifting. But I don't ride in salty conditions these days like I did when younger so don't think much about this on my current bikes. Andy