There are various safeguards in the law that make this trade more appealing to the public. Since the monopoly rights are so strong (there is no "fair use", for example), there is a high level of scrutiny before granting them. And there are high standards that must be met ("subject-matter eligibility", "novelty", "non-obviousness", "definiteness", "enablement"). And even after a patent is granted, it is contestable (but, litigation is expensive). The big safeguard is that patents are limited to a term of 20 years (in the U.S.) and after that the invention is dedicated to the public.
I am pretty sure that the 20 year term is non-ideal. For some types of inventions (e.g., those requiring only a small investment of time or money to innovate) society may be granting inventors too long of a term. For other types of inventions, the term may be too short (e.g., where an innovation required a huge amount of investment). As you pointed out, the effects on society are hard to calculate.
Because the rules are "one size fits all", I am pretty sure we don't have an ideal system. However, I don't know if adding more rules would make the system better or worse. At least interested parties can petition for changes either through the courts or through the legislatures.
I will say that you've sort of missed what I think is the important part:
We as a society have decided that it's acceptable to legally bar medical practitioners from performing life saving treatment of sick individuals.
The only explanations I've heard for why that might not be crazy has unfortunately been simple and hand-wavey. Specifically I've heard that patents protect innovators, and the idea is that protecting innovators by intentionally granting them a limited monopoly on the use of their invention will create a society more likely to produce new innovations. The idea is that despite clear negatives, patents offer a net benefit to society.
The problem is I can easily imagine scenarios for either side of that argument, but I've never heard a comprehensive argument in favor of the current way of doing things. I also can't help but notice that patents often protect the establishment by granting the wealthy more monopoly power. Given that the legal system is in many ways captured by the wealthy establishment, I question whether the patent system continues to exist because it is truly beneficial to all or because it benefits the elite that also extert significant power over the legal system.
If the latter were true, then it could also be said that patents are another example of the establishment hurting the masses for their own gain. And in this case (again, as you pointed out the practical effect of this example may be small), the patent system is creating a risky legal situation for those who would try to provide medical care for sick members of our society.
As an anecdote, 3D printers were $30k until several major patents expired. Then small companies formed and in less than 10 years we created excellent 3D printers that cost $329 (I just bought one of those).
I can't help but wonder what the cumulative effect of artificial monopolies is on our society. Because it's invisible it's hard to calculate, but it's clear to me the effect is large.
I'm open to any insight into these matters. My plan is to promote the voluntary open sourcing of engineered works, but I'd sure love to stop supporting the patent system in the first place (I think).