This is something FFTW got right. Just license it as GPL, with an option to pay for a more restrictive license. It's totally open, and the university (MIT in this case) gets any licensing fees they would have gotten were it restrictively distributed. Copyleft works for you!
The only missing element is an attribution clause for research done with the software. That and the GPL isn't so helpful for research binaries (as opposed to libraries), as other researchers are unlikely to redistribute their modified code.