A lot of editors seem to miss the difference between regiment and regimen.
While I tend to agree with you that an author should keep these two words separate, unfortunately the usage isn't quite as distinct as you suggest. From Dictionary.com, quoting Random House 2016:
1. Military. a unit of ground forces, consisting of two or more battalions or battle groups, a headquarters unit, and certain supporting units.
2. Obsolete. government.
verb (used with object)
3. to manage or treat in a rigid, uniform manner; subject to strict discipline.
4. to form into a regiment or regiments.
5. to assign to a regiment or group.
6. to form into an organized group, usually for the purpose of rigid or complete control.
In other words, as often happens, the military usage of "regiment" is a jargon term; in casual usage the word regiment also has meaning almost identical to "regimen", which is itself a jargon term from the medical field.
You could compare this to the difference between "gun" or "boat" in common usage. In the Navy, a "boat" goes on a "ship". In the infantry, a "gun" refers to field artillery, soldiers carry "rifles" or "pistols".
So when writing military or medical fiction, the distinction between "regimen" and "regiment" should probably be observed, but in general fiction, regiment is fine with either meaning.
By the way, I checked the words in the OED. The meaning of regiment as "control over oneself" actually predates the military usage (1483), and in the medical sense as early as 1425; the shift to regimen for the latter usage began in 1525, while the military definition doesn't show up until 1617.
So basically it looks like the split between regimen and regiment happened for the specific fields, but never fully occured in general usage.