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The only reliable idea popping into my head for now is to write an ASM hook to wherever the main battle loop is, loop through the opponent's party, check to see if they only have one pokemon with more than 0 HP. If true, toggle this catchable flag, and then branch to the rest of the main battle loop. You could probably have another flag that you can toggle with an XSE script that, when true, this check is run, otherwise jump straight to the main battle loop (so you can choose which trainers have catchable pokemon).
I personally have no idea where this hook would be so you'd need a fair amount of research to go this route beforehand.
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