In 1678, Murray temporarily lost royal favour by counselling moderation concerning the measures taken against the Covenanters, but fought vigorously against the 9th Earl of Argyll in Argyll's Rising of 1685 and was instrumental in defeating him.
Murray was described by Lord Macaulay as "the falsest, the most fickle, the most pusillanimous of mankind", regarding Murray's indecisive position surrounding the succession of William of Orange and the deposition of King James."