Yes, a very good point! It’s a point I now wish I would have addressed in the article. In the field, I have observed this same concept with users many times. They become so familiar with a bad interface, they adapt and it becomes the norm. When you introduce a new interface to them — one that follows sound usability principles — they often lament the change desipte the interface having a higher usability rating.
We can see this prinicple at play in every day technologies. Consider your average remote control. Most of them are poorly designed, but we learn to use them after years of owning the same device. If someone were to improve the design and change the layout of the buttons, we would then struggle with the change.
The one item to consider here is new users. New medics will enter the field and new doctors (and nurses) will enter the field. They will either have to learn new software that is poorly designed or designed using sound usability principles. I have worked in places where employees would either accept a job or not accept a job due to the healthcare software used at the organization. In medical school, there has been a recent to push to begin educating doctors and nurses in the use of EHR software — actual classes devoted to the subject. So, we have whole segment of users we must consider in this respect when designing and developing software.
Either way, we stand to lose some users. Either way, we will piss someone off by changing or not changing the software. I see the change as inevitable, but certainly empathize with your point as it is always a primary concern we deal with on UX teams.