Am I understanding you that they're laid flat 7-1/4" wide by 2-1/2" high? If that's the case, you cannot even get the pipe in the floor. You'll have to raise the floor.
If I'm misunderstanding, then how many joists do you have to go through? If only one, maybe two, you could maybe header off the joist and sister up some adjacent ones to make access. What kind of span are you looking at here?
I know very little about wall mount toilets, but it could be an option. I think you need quite a bit of room in the wall, though, for the hanger and drain assembly.