Dr Johnson kicked a large rock and said, as his foot rebounded: “I refute it thus?”!
AFAICS, the only way to render this faithfully is the way I just did. In other words, you really do need the punctuation both of the outer sentence and the inner sentence. By extension, the only logical approach for the original sentence would be:
Dr Johnson kicked a large rock and said, as his foot rebounded: “I refute it thus.”.
On a different note, might I use this moment to complain about American books not closing quotations, if they continue on onto a new paragraph, and then opening them again? I.e.:
John said: "I have two things to say.
"One of these things is this.
"The other thing is this."