Where's the line between benefiting the creator of a tool and putting a wall up around a tool that can benefit all of humanity?
Without patents there's a risk that the creator keeps their invention secret forever and then it's forgotten. This could still happen today, but if the invention details are ever leaked you'd have no ability to stop others from making and using it and no ability to demand money for it (though you could sue the person who leaked it, but only civilly).
I think in cases like this where it's unlikely to have been a trade secret anyway the justification that the patent is in the best interest of the public or is 'promoting the progress of science and useful arts' is harder to make. This is especially true when the research is the result of public funding (though I'm not sure that was true in this case).
Company or private person submits a patent.
The government determines what they would pay to make the technology open (i.e., benefits to society). This is similar to the process of determining the subsidy to develop new technology.
Government makes an offer. Submitter can accept or reject.
If rejected, the patent remains secret, but other companies have the right to independently invent the same technology.
If accepted, the patent is published. If other companies want to use the technology, they will need to buy a license from the government. Submitter has no control over who may or may not use the technology.