The rule book can't and shouldn't be expected to anticipate and cover every possible outcome. Not unless we want a rule book that is a million pages thick.
It would seem that if the two-throw penalty for a misplay is viewed as inadequate to address a situation like this, then it is the situation that needs to be anticipated and adjusted rather than the rule. If the difference between the two pin positions is such that a player can misplay the hole and gain an advantage (intentionally or not), then measures should be taken to prevent that from happening.
Like David suggests, the basket that is not supposed to be played could be covered or removed for the round. Or, if different divisions are playing different locations within the same round/flight, then as others have suggested, groupings should be set up to avoid having players within the same group playing to different pins. That's just an invitation for confusion like happened in the OP. Or, the TD could seek and perhaps get approval for a special condition for that hole where the penalty for misplay is more than the rule book dictated two throws.
The key in any of those solutions being that the TD and/or staff be proactive and anticipate potential problems. Of course, one can't anticipate everything, but misplays like this are ALWAYS going to be a possibility on courses where there are multiple permanently installed targets on each hole. No reason at all that precautions can't be taken on such courses to if not totally prevent, then at least greatly reduce the chances of misplay. It can't all be left to the rule book to solve post-hoc.
It would seem that if the two-throw penalty for a misplay is viewed as inadequate to address a situation like this, then it is the situation that needs to be anticipated and adjusted rather than the rule. If the difference between the two pin positions is such that a player can misplay the hole and gain an advantage (intentionally or not), then measures should be taken to prevent that from happening.
Like David suggests, the basket that is not supposed to be played could be covered or removed for the round. Or, if different divisions are playing different locations within the same round/flight, then as others have suggested, groupings should be set up to avoid having players within the same group playing to different pins. That's just an invitation for confusion like happened in the OP. Or, the TD could seek and perhaps get approval for a special condition for that hole where the penalty for misplay is more than the rule book dictated two throws.
The key in any of those solutions being that the TD and/or staff be proactive and anticipate potential problems. Of course, one can't anticipate everything, but misplays like this are ALWAYS going to be a possibility on courses where there are multiple permanently installed targets on each hole. No reason at all that precautions can't be taken on such courses to if not totally prevent, then at least greatly reduce the chances of misplay. It can't all be left to the rule book to solve post-hoc.