It is rational to Follow The RA even if it contradicts an ATC instruction.
Of course it is rational to follow the RA and blend everything else out. This will well be the action that comes nearest to the mathematical "rationale".
Problem is, as soon as you introduce humans into your system, the question of rationality becomes a lot wider. A course taken by a human will be rational, if he acts acording to the limited information he has. If he chooses, the best way for him to solve his problem will be course A, course A will be a rational choice. You cannot decide on the rationality of a humans actions by looking at the outcome alone - the pilot's cristal ball isn't near as good enough for this ;-)