You're asking why it's a problem that the government excludes the majority of scientists from applying for funding. Wouldn't you just want the best teams and proposals?
I feel like the academic freedom comments are put out there mainly to try to get non-scientists at universities interested in this issue. To me, this is simply about spending tax dollars effectively. It does outrage me when I see a professor getting a big government R&D contract to research something I've already done, or could do at a much lower cost, when I didn't even have a chance to make my case.
I'm currently an industrial scientist, and have been a government scientist. In both of those positions, I am prevented from fully competing with academic, tenure track researchers for government R&D funding. Why?
The only special thing tenure track professors do is bestow PhDs on students. One, we don't need more PhD students; half of those kids should be going to medical school, really. Two, I still train and advise students as a non-tenured scientist, I'm just not the guy who puts the hood on them at graduation.
I compete with academics for patents and private investment. There is nothing stopping an academic from applying for the small business set aside funds, signing a research contract with a government lab, or competing with me for an investor's funds. But unless I'm in a tenure track academic position, I cannot even be considered for many government R&D grants. That's pretty stupid.