http://www.heritage.org/constitution/#!/articles/1/essays/62/bill-of-attainder
The Framers forbade bills of attainder as part of their strategy of undoing the English law of treason, and to contend with what they regarded as the most serious historical instances of legislative tyranny by state or national legislatures. Professor Raoul Berger argues that the bill of attainder clauses (see also Article I, Section 10, Clause 1) protect only against legislative actions that affect the life of the individual, not his property, which was the province of bills of pains and penalties. Beginning with Chief Justice John Marshall, however, the Supreme Court has insisted that "a Bill of Attainder may affect the life of an individual, or may confiscate his property, or may do both." Fletcher v. Peck (1810).
Marshall and his successors saw the Bill of Attainder Clause as an element of the separation of powers. As the decisions of the Court in Marbury v. Madison (1803) and United States v. Klein (1871) made clear, only a court can hold a trial, evaluate the evidence, and determine the merits of the claim or accusation. The Constitution forbade the Congress from "exercis[ing] the power and office of judge." Cummings v. Missouri (1867). In United States v. Brown (1965), the Court specifically rejected a "narrow historical approach" to the clauses and characterized the Framers' purpose as to prohibit "legislative punishment, of any form or severity, of specifically designated persons or groups."
It would be interesting to see this litigated. In practice, I think the courts would rule against any Congressional action which did this to a certain person for a specific reason. However Congress is probably able to pass legislation mandating general compensation rules (power of the purse). But to single out a particular employee or a group of employees by name and drastically cut their compensation probably is not constitutional at all.
Because the Constitution prohibits Congress from cutting US judiciary compensation, the courts might be a little less alert to this issue than otherwise:
https://www.law.cornell.edu/constitution/articleiii
Section 1.
The judicial power of the United States, shall be vested in one Supreme Court, and in such inferior courts as the Congress may from time to time ordain and establish. The judges, both of the supreme and inferior courts, shall hold their offices during good behaviour, and shall, at stated times, receive for their services, a compensation, which shall not be diminished during their continuance in office.
Or the courts might look at this as a guideline, and argue that cutting salaries of those that the Executive has lawfully appointed is an impingement on the constitutional power of the Executive even if it is done in a way that does not amount to a Bill of Attainder.
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