Well, I don't really like that: it just doesn't look nice to me. I would suggest one of the following:
Dr Johnson kicked a large rock and said, as his foot rebounded, “I refute it thus”.
You've chosen not to quote the full stop. There's no law that says you have to include everything in the quotation, right?
Dr Johnson kicked a large rock and said, as his foot rebounded: “I refute it thus.”
This also works if the quoted sentence ends with a question or exclamation mark.
It's a shame that punctuation of human languages can't be logical, but it seems that we're stuck with inconsistent requirements and messy compromises. Cases like the following really confuse and annoy me:
“On the other hand[,]”[,] she said, “we could wait till dark[.]”[.]
(Should that depend on whether the original spoken sentence would, if written, contain a comma after "hand"?)