No Senator or Representative shall, during the Time for which he was elected, be appointed to any civil Office under the Authority of the United States, which shall have been created, or the Emoluments whereof shall have been encreased during such time ...One potential solution is to roll back the Secretary of State's cost of living increase, which took effect last January, although the legislative directive for that increase was enacted during the 1990s.
That would likely satisfy the intent of art. I, § 6, cl. 2, but would still seem to violate its plain language: "shall have been encreased" doesn't appear to allow for just a net increase, but rather any increase that took effect during "the Time" (Clinton's tenure) whether or not there was a subsequent decrease.
On the other hand, according to Super Duper Strict Construction,* Mrs. Clinton is not a "he."
* h/t Arlen Specter.