I wouldn't give up on it that easy. A good soaking with rust converter would knock down 99% of the spots. Sealing it up with an epoxy primer would do the rest. If it's straight and will work for you use it, no one is going to see it anyway once the body work is done. I did this same thing to my '73 when I pulled the vinyl roof off it in 1979. Cleaned it up, did a little lite sand blasting and buried it primer surfacer. It still looks good to this day. If it's prepped right you will have no problems with it.
The thing you don't want to do on a build like this is get caught up in the "everything must be perfect" whirl pool. Everything doesn't have to be perfect and trying to get to that point will bury you. If it's never going to be seen in the finished product, make it presentable/usable and move on.