...and how does the patent help this? It sounds you had researchers paid on a grant, and a drug company that sold the fruits of that research. I am not seeing the case for a patent here at all.
If Northwestern did the research with its own money (which does sometimes happen, I think), then it is good that Pfizer had to pay Northwestern for the research, because this funds more research. The patent is just the legal mechanism that makes Pfizer have to pay as opposed to getting the research for free.
In some cases, the government funding issue is relevant. Not in all cases.