From the Case, it appears that the logic is that B has compelled A to break the first part of Rule 30.4, but A breaks the last part of Rule 30.4 through her own actions, so 64.1(a) does not apply.  

I agree that the Case could be very unfair to A in a situation where they become a victim of a rule as a result of keeping clear of a boat breaking a rule.

Correct - A breaks 30.4 by starting in the re-sailed race.  There's no remedy for that - it fails the "through no fault of her own" test in 62.1.

Bottom line - if you're black-flagged - for whatever reason - and the race is recalled or abandoned after the start - you do not start in the re-sail of the race.  Period.

I acknowledge the logic and equity would suggest that A should get some sort of redress, but unless she was damaged by B, she can't make it over the hurdle of 62.1.