First, is that Congress technically did NOT increase the wages of the Secretary of State, the only thing that happened was Bush implemented a pay raise to reflect inflation under a pre-existing law permitting such pay wages. When this happen Clinton was a Senator, she did NOTHING to get the salary increases but also did nothing to get it decreased (The underlaying law permits Congress to reject the pay increase within a set time period, no such vote occurred). This is based on the understanding that the issue of pay for such position was intended in the Constitution to be the exclusive power of Congress AND all Congress did when it gave the President the right to increase salaries to reflect inflation was to preserve salary NOT increase it (No REAL Increase in salary, NOT a problem).
Second, to be on the safe side, Hillary agreed to take the job at the salary the job had WITHOUT the pay increase. This has been the norm for members of Congress who takes positions in the Executive branch since the President Nixon appointed Senator Saxby to a position in his cabinet in the 1970s (Through the first "Saxby-Fix" was in 1909 under President Taft). Given that the intent of the Constitutional provision was to prevent Congress from increasing the pay of a position and then using their political power to get appointed into the position with its high pay, the option of taking the position at the pay it was BEFORE the pay increase occurred has been viewed as constitutional since the 1970s (When a Democratic Congress voted for the "Fix" so that a Republican could be a member of the Cabinet of a Republican President).
In simple terms, Hillary's appointment to be Secretary of State is constitutional given she took the position WITHOUT the pay raise that occurred when she was a Senator. First, she did NOT vote for it, and second she took the position without the pay increase. Thus the INTENT of the constitutional provision was followed. She did NOT vote for an increase in pay for a position so she could take that position AND its increase pay.
The roll back of the Secretary of State's salary:
http://www.chicagodefender.com/article-2699-secretary-of-state-salary-cut-for-clinton.html For more on the "Saxbe Fix" see:
http://en.wikipedia.org/wiki/Saxbe_fixOne last note, the Courts will NOT want to intervene in this dispute, while they might cite "Standing" the real reason is this is a "Political Question" best settled by the Congress. If Congress does NOT want to contest this point, neither will the Court.