I would try the tiletypes plugin in dfhack. you should be able to change the tiles to open space or to a dig-able rock type or even right into obsidian stairs and walls I think.
I'm currently four levels into the SMR! This method works like a charm. There is a slight bug in the old 0.5.15 version of dftiletypes.exe which crashed my game, but only if I tried to place obsidian in already revealed space. It probably had something to do with the 'paint hidden 0' command not working. Since I had set things up initially for the 1x1 bore hole method all of the SMR was still in its' default unrevealed state. Placing (or painting) hidden obsidian walls had to be done blind but that was not overly difficult.
I only placed obsidian on SMR squares. Some of those where SMR floors with magma. Interestingly, the magma would remain 'on top of' the newly placed obsidian wall. When I'd channel out the square it would become a ramp with 7/7 magma, which I'd deal with in the normal manner either by draining the magma away or by using water to turn it into obsidian. Also, if I channeled out an adjacent square the magma 'on top of' the obsidian wall the magma would drain out of that square leaving the wall with 1/7 magma which would dry out to 0/7 as normal.
Alas, no dwarfs martyred themselves punching this new 4x4 stair column through, Two miners did almost starved to death when flowing magma cut off their only path back to the surface. The magma dried out in time for them to reach food before they died.