Your door doesn't look too bad except for the windows. You could remove them and cut out the rusted metal around them, then rivet sheet over the openings on the outside. I did this, just with the lower window only (top one was unrusted). Yesterday I finished up insulating the door on the inside and relocating the latch to the new interior panel, so the door is flush with the rest of the back wall and I can have my bed frame right up against it.
Your idea to frame the opening and skin it and add a new access hatch is good, too.