I'm not sure what you mean, all of those agencies are formed under the constitution and the systems that support them are also abiding by the constitution

The Constitution states, 'no Bill of Attainder or ex post facto Law shall be passed'; to the extent that those executive agencies' enabling legislation permits ex post facto regulations, that legislation is unconstitutional.

The Government can simply ban the use of that software without a license set at a future date (i.e. 1/1/2017).

New Regulation -> Future Date -> Ex post facto claims don't happen.

That is the process my original comment intended to imply.

They're definitely not. They've resisted due process for some time. NSA's reps even argued in Jewel case that judicial branch shouldn't be allowed involvement at all. Which is sort of the status quo for intelligence agencies and courts. Prosecutors similarly have a combo of broad powers, immunity in common abuses, and virtually no accountability. The government as it exists certainly doesn't run in the framework of the Constitution except in a partial way.