You don't have to work on something directly to create a violation. Electrical systems are usually interdependent. The nature of contracting and work scope makes us want to think of these systems as separate, but its not always possible. Prior to modification, this was a 1950's system, now its not - its a mix between what was once allowed and what is required now. Anytime there is a grey area like this, I think it requires due diligence.
Imo, the contractor has a duty to understand the impact of their work. This certainly doesn't mean he has to replace the entire building to bring it to code, but we are talking about a couple of GFCI's... I draw the line where it is reasonable, ethical and I am not somehow liable.
The violation arises because its not a like-for-like replacement and the contractor could have employed GFCI breakers. Since the contractor doesn't necessarily have to use GFCI breakers (and said branch-circuits do not have GFCI protection), its a lack of oversight and possibly negligent from a liability standpoint. If this was somehow willful safety deficiency, and someone got hurt, I am 100% certain a county level permit wouldn't help protect anyone.