Caveat: I don't know if this was his reasoning, but it's certainly plausible. The four Nay votes in the Senate were cast by Carl Levin, Jack Reed, Bernie Sanders, and Sheldon Whitehouse, all of whom are supporters of human rights.
More detail: Our story begins in 1974 with the Jackson-Vanik amendment. From the linked Wikipedia article:
The Jackson–Vanik amendment to the Trade Act of 1974 is a 1974 provision in United States federal law intended to affect U.S. trade relations with countries with non-market economies (originally, countries of the Communist bloc) that restrict freedom of emigration and other human rights.
The amendment, named after its major co-sponsors Henry M. "Scoop" Jackson of Washington in the Senate and Charles A. Vanik of Ohio in the House of Representatives, both Democrats, is contained in Title IV of the Trade Act of 1974. The Trade Act of 1974 passed both houses of the United States Congress unanimously, and President Gerald Ford signed the bill into law with the adopted amendment on January 3, 1975. Over time, a number of countries were granted conditional normal trade relations subject to annual review, and a number of countries were liberated from the amendment.
. . . .
The amendment denies most favored nation status to certain countries with non-market economies that restrict emigration, which is considered a human right. Permanent normal trade relations can be extended to a country subject to the law only if the President determines that it complies with the freedom of emigration requirements of the amendment. However, the President has the authority to grant a yearly waiver to the provisions of Jackson-Vanik, and these waivers were granted to the People's Republic of China starting in the late 1970s and in later decades, to Vietnam and Laos.
What does this have to do with the Magnitsky Act? Well, for some reason that I'm not privy to, the Magnitsky Act wasn't presented as a stand-alone piece of legislation. Instead, per
the Wikipedia article on the Magnitsky Act:
In November 2012, provisions of the Magnitsky bill were attached to a House bill (H.R. 6156) normalizing trade with Russia (i.e., repealing the Jackson–Vanik amendment) and Moldova.[11] On December 6, 2012, the U.S. Senate passed the House version of the law, 92-4.[8]
I'll hazard a guess that, in the Congressional sausage-making, a deal was cut. On the one hand, there were legislators who wanted to punish the specific individuals who'd been involved in Magnitsky's murder. (The Obama administration later released a list with 18 names.) On the other hand, there were legislators who, probably responding to corporate pressure, wanted to facilitate trade with Russia in general, because there was money to be made. Four Senators (and 43 Representatives, mostly Democrats) disagreed with the resulting compromise.
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