If replacing the entire floor is within your skill and experience (I guess it is, as you are considering it), I would suggest that it is the best way to go. You will already be aware that you may find that at least a few other bits need replacing too, as is usually the case with rust repairs on any car. You are obviously aware of the rear valance and subframe mount stiffners etc, and will be having a close look at the wheel arches, body sides, closing panels, etc. All I am saying is, don't be too disappointed if more than you would like needs to be replaced. Doing it right will add value to the car.
Personally, I hate patching large panels due to the amount of work involved, and prefer complete replacement, so I may be prejudiced slightly. I am quite sure that some very competent people on this forum would take the opposite view. It depends on how we all like to spend out time, as compared to money. If you put a sensible value on your time, replacing complete panels will almost always win, but if you consider your time to be free, patching may win, if you don;t need to use too much gas and other consumables.