Apparently, several legal commentators have picked up on the Hillary Clinton v. Emoluments Clause issue. There is a discussion in the New Republic here or the Daily Kos here. The Daily Kos has the best and most complete discussion with excerpts from the Constitutional Convention in 1787.
This issue comes up from time to time. When Clinton wanted to appoint then Senator Lloyd Bentsen as Treasury Secretary the reaction of Congress was to pass a special act to allow it. Then president George H.W. Bush signed it into law (on January 19, 1993 no less) thereby allowing the new President Clinton to have Bentsen head Treasury. (You may remember Bentsen from the vice-presidential debates of 1988. He said "Senator, you're no Jack Kennedy" to Dan Quayle when Quayle tried to compare himself to JFK. Don't believe it? Go here to get the transcript.)
The original Senate bill and a history of the bill can be found by searching the Library of Congress legislative search engine Thomas at, http://thomas.loc.gov/. You will need to remember that the 103rd Congress was in session in 1993. Just choose the right Congress, enter the word "emoluments" in the search box and the history of this bill (and what the next Congress needs to do make sure that Hillary can be Secretary of State) becomes clear.