At the time, I did not have the skills or a welder. I found a guy who fixed it all (on my FJ55) and got it all ready for paint, for $300. Screaming deal. At the time, the headliner in my '55 was junk, so that was one less thing to worry about. Since then, I have done extensive welding on 'cruiser bodies, and wouldn't hesitate to do this.
Any time you see rust partway up the roofline (the vertical portion of the roof cap) of a '55 or '60, it's almost always due to a leaky rain gutter (bad caulk in the bottom of the gutter), and water soaking into the roof insulation and wicking up the side of the roof, causing it to rust through from the inside out. A buddy of mine in Houston has an '83 FJ60 with this same problem, and his gutter caulk was totally destroyed by the Texas sun.
If you do this work yourself, you can buy a used 220v MIG welder ($600-750), some steel ($35 or so), some good primer, a Harbor Freight HVLP paint gun, and likely have it 'ready to paint' (if you want a pro to do it) for less than $1K.
Also, shops may be tempted to just re-apply filler. You want an all-steel repair, and then you want to spray the backside with cold galv. compound and be sure that water never gets to the back side of your repair. If you have a shop do it, be sure you can SEE the work before they cover it with filler and paint. Check out my 'Restoring on a budget' article here:
Toyota Trails 2014-4 JA | TLCA to see how I fixed the rust on my FJ62. What you'd be doing isn't much different.