You will need to:
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average the damage of the agile attack
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average the damage of the non-agile attack
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multiply both by their chance to hit (taking crits in consideration). You can find an average AC per level here.
On your reading of the rules: The agile weapon list has a lot of weapons that were used alongside bigger weapons irl (dagger, wakizashi, main-gauche). I assume your reading is correct.