There is no necessary loss of academic freedom. Paying a competitive salary doesn't make research commercial -- the university is trying to retain researchers not turn a profit on the research.
Depends on the university. Most claim ownership of researchers' inventions and have ambitions of profiting from them (many stumble at the commercialisation/monetisation step). For example, Stanford has reportedly made hundreds of millions off Google's PageRank algorithm, because Stanford owned the patent, not Larry Page. That's a good incentive not to work as a university researcher.
Another way to look at it is researchers are getting somewhat angelic investments from schools.
Really universities need to find ways to capitalize on their knowledge base to help pay salaries. They also need to reduce overhead... Many schools have several disjoined IT and sometimes HR departments.
If universities had to play by the cutthroat logic of the market as a consequence research or teaching that is not profit oriented would have to die out, or tuitions rise to levels that put immense pressure on individuals and the public purse.
This is a dystopian scenario where academic freedom, basic research, and the non-commercial nature of research is completely lost. This is not something we should be going for, instead we should appeal to highly trained researchers to maybe think about the public good that is at stake here. People like Bengio show that it is possible. A future where essential AI research is commodified is a nightmare scenario.