That's the point where the analogy breaks down though, because the actors in the patent case are private actors rather than sovereigns. So if you e.g. abolish software patents the whole problem disappears, but nobody can "abolish" nuclear weapons because they're a consequence of the laws of physics rather than the laws of the United States.

If humans had the power to amend the laws of physics to make nuclear weapons impossible and yet nuclear physicists lobbied against it, then they would be in the same position as patent lawyers.