Actually, as an owner of a 68 MGB and someone who had to replace the floor pans myself, I disagree with your first conclusion: the holes in the floor probably were not CAUSED by the metal 'floor' that was added on, they were the REASON the person tacked on that added floor. Rather than remove the original floor and weld in a new floor pan on each side, they chose to hide the issue with an additional metal piece.
The actual floor replacement is not that hard if you can buy new floor pans. Just cut out the old (you don't even have to cut it all out, just the worst parts) and then MIG weld in the new floor. Seam seal and paint with a good rust-binding primer and you are done.
Even I managed to do the job and I never welded sheet metal before (just 1/8" angle iron frame type stuff). In spite of that I managed to do a decent job once I read the proper welder settings and practiced on some scrap.
In other words, FIX IT. It's not hard, and you'll be most pleased with the job complete.
Oh, one other p.s. to my previous post... I've watched you work on this car, and it's nowhere near as rough as you think. For one thing, the seats, door panels and dash indicate it's been garage stored and is actually in pretty decent shape.
The floors are again pretty great. Except for the perforation on the driver's side and maybe a hole on the passenger side, that sheet metal is pretty darned good.
Restore the thing. Not 'concourse' finish, but remove the rust, replace only as much of the floor as is gone and badly rusted (i.e cut back to good metal and then cut the pan to fit and weld it in).
Then go drive the little car and have fun. As you find problems, fix them and carry on.
I have a 1960 Bugeye Sprite which was rough when I bought it, I ended up making a floorboard weld repair on the passenger side. Rather than recarpet it I decided to just make rubber floor mats which snap into the floor as originally designed. It is easy and quick to just unsnap the mats and hose them off when they get dirty, and most importantly they don’t hold moisture like rugs causing new rust issues over and over. Best of all the mats don’t dampen that beautiful exhaust roar that resonates with the car. As far as restoration is concerned, my wife has a perfect MGB which scares the daylights out of both of us because it is a genuine piece of history. I have no reservations about driving my Sprite and I have 3 engines and transmissions standing by, almost like a racing team, these cars are practically the definition of fun!