The truth is that, as we have seen over the last four years of reading Daf Yomi, the rabbis very often depart from biblical law, even to the extent of completely rewriting it. Exactly when in Jewish history the practice changed from reciprocal injury to the payment of a fine is unclear, but by the time the mishna was compiled, in the first century CE, the change was already well-established. However, it is a fundamental principle of the Talmud that such revisions can never be acknowledged as revisions. After all, if the Bible is the word of God, no human court can modify it. What it can do, instead, is to reinterpret the Bible so that it says the reverse of what it seems to plainly mean. Such reinterpretation is authorized by the idea that the oral law, as recorded in the mishna, is of equal antiquity with the written law because both were given to Moses at Sinai.Earlier Daf Yomi columns are noted here and links.
UPDATE: The immediately following post above is also relevant: The Mishnah on the Lex Talionis (Law of Retaliation).