JMO, but I don’t think CJ Roberts ever had any intention of throwing out the whole bill.
I think he was initially in favor of removing the mandate and leaving the rest of the law intact. When the conservatives rejected his argument, he jumped sides and used tangled reasoning to get around his main objection, overreach of the Commerce Clause.
It’s FUBAR anyway you look at it.
Here's a story that discusses it:
Sunday on Face the Nation, Jan Crawford of CBS News said that two reliable sources told her that Roberts originally voted, in late March, with the four conservative justices to invalidate the individual mandate. According to Crawford, Roberts suddenly changed sides some six weeks later and then resisted “a month-long desperate campaign by the conservative justices to bring him back to the fold.”
I’ve learned from my own sources that after voting to invalidate the mandate, the chief did express some skepticism about joining the four conservatives in throwing out the whole law. At the justices’ conference, there was discussion about accepting the Obama administration’s argument, which was that, if the individual mandate was removed, the provisions governing community rating and guaranteed issue of insurance would have to go too but that the rest of the law might stand. The chief justice was equivocal, though, in his views on that point.