I believe I'd save as much of the original panels as I could, cut the rust out and replace it. It's only going to get worse - rust never sleeps - this car is a keeper in my estimation, so bite the bullet and get 'er done. I had the opportunity to work on a true survivor car several years back - there were some imperfections in the 100% original paint (quarter panel at the rear window scratches, front stripe, door stripe, front header panel) - a 7000 mile '68 SS 350/295, Corvette Bronze - the then-owner decided to touch it up, and it actually worked - you really could not see the areas that were repainted, the overall effect was outstanding. True, it should have been left alone, but the owner wanted perfection. Point is you can fix the issues without detracting from the car, and help preserve it for the years of enjoyment to come.
The rest of the story - fix was not cheap, $1100 in 1995. Painter was well renowned local guy, painted many of a local collector's Yenkos and others, one of the best I have seen. With color matching today as high tech as it is, color blending shouldn't be a concern if you use the right guy.
Just my 2 cents -