Don't think about it too hard, If anything Obito ENTIRE body would be crushed then. Think about it, after Rin and Kakashi exited the grave of Obito, the cave collapsed in. Meaning his WHOLE body would be crushed. If Kishi here is showing that tobi has one eye, then it is very possible that Both sides of his body survived.
To explain how he got the other sharigan when kakashi is suppose to have that side, when tobi lost it to konan. "Madara" or Tobi helped slay the entire uchiha clan with itachi. Very easily he could have collected a few from them if he wanted to.