We need to establish who are the real owners of the software produced by people receiving government grants. There is a very well established precedent in the computer industry that requires any employee of a commercial company to sign over the rights to any intellectual property he or she creates while on company time, or when using company resources. I don't hear too much complaining about that requirement, it is almost routine in most employment contracts. People in the academic world, however, seem to view the work they do as "their own" work, yet it is paid for by my taxes. I am their employer, they should follow the clear precedent set by almost all other organizations, and turn their work over to me and the rest of the owners; we own their work because we finance their activities.
The employees of the goverenment agency that bestows the grant are also MY employees, but I have tacitly given them the right to represent my interests in these matters. The license to apply to government funded software should be defined by some qualified government agency. The authority we have granted to these agencies includes the right to collect - or not collect - money or ongoing fees from any entity that wants to use the results of that work. There is no obligation on the part of the government to give away any of the intellectual property it funded; their obligation is to represent the taxpayers best interest as they view the issues. I don't want enemies of the United States to benefit from my tax dollars, so I'd rather allow the agency in charge of the grant to use their best judgement to control the release of that IP.
If researchers want to use proprietary software in their projects, and if they want to use government money to pay for it, then they should go through the appropriate government agency and present their case. If they want to mix work from private and government funding, then they have the obligation to keep the intellectual property separated by owner unless the government agency that funded their project sees fit to allow them to grant private entities beneficial access to that IP. We are a representative democracy, and we need to have faith in the organizations we put in place to administer our affairs.