Malachi is a short book, and there is only one passage which is directly about divorce, 2:13-16, with 2:16 being the key text here. Milton cites John Calvin's translation, given in his commentary on the minor prophets (Praelectiones in Duodecim Prophetas Minores; Geneva, 1559), which begins:
Si odio habeas (quisquis odio habet,) dimittat (i.e. uxorem) dicit Iehovah Deus Israel
The parentheses here are a clue that the original text might not be totally clear. This might be put into English as something like:
If you hate [or: whoever hates] let him dismiss [his wife], says the Lord God of Israel
If you read virtually any other modern English translation, you'll see the same passage rendered differently:
For I hate divorce, says the Lord, the God of Israel. (NRSV)
"The man who hates and divorces his wife," says the Lord, the God of Israel, "does violence to the one he should protect" (NIV)
"For the man who does not love his wife but divorces her," says the Lord, the God of Israel [...] (ESV)
This reflects difficult readings in the text of Malachi as we've received it in Hebrew, Aramaic, Syriac and Greek. To summarize a complicated situation, the Masoretic Text (a consensus Hebrew version) appears to condemn "the man who hates and divorces", but has some grammatical oddities. The Septuagint (an early Greek edition based on similar sources to the MT) expresses a similar idea with different grammar, as "if having hated, you divorce", and was followed by Jerome in his Latin translation. But the Targum Jonathan, an Aramaic text that by Talmudic tradition was composed "from the mouth of Malachi" among others, has "if you hate her, divorce her", and condemns those who fail to do so.
Overall, there are intertwined difficulties of making sense of the grammar that we have received in different versions, and the theological sense of what Malachi meant to say. It is tempting to read in a condemnation of divorce, or to harmonize it with other passages such as Deuteronomy 24, but in any case this is a thorny piece of text, which remains problematic to this day.
Calvin's reading, which he expounds further in his commentary, is that the passage gives permission to divorce in the context of a polygamous society; he thinks it is worse to retain the original wife in a loveless marriage while adding a new wife, than it is to let her go. Whether or not this is textually or theologically correct, it was influential for Reformation translations into English, such as the Geneva Bible of 1560 ("If thou hatest her, put her away, sayeth the Lord God of Israel").
In 1611, the King James Version preferred the other reading ("For the Lord the God of Israel saith, that he hateth putting away"), and since that was the officially sanctioned translation, it set the standard for most translations to follow - at least up to the period of critical textual reassessment in the 19th century.
Milton's opinion of which was the "best translation" may have had some influence, as he presented his book to the Westminster Assembly of Divines in 1643. Some of the participants later wrote a commentary (Annotations upon all the Books of the Old and New Testaments, by the Assembly of Divines; London, 1651) in which they give "if he hate her, put her away" as an alternate reading.
