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I do not know what is exactly feasible, but conceivably this effect could limit itself to draining charges from ability headers of type 3 (magical ability), and only destroying the item if the word at 0x24 in the ability header is not 3 (i.e., don't destroy recharging items) and if said charge count reaches 0 as a result of the drain.
243 (0x0F3) Item: Drain Item Charges 
Parameter #1: Item Type
Parameter #2: Number to Drain
Magical items matching the 'Item Type' value on the targeted creature(s) will have their charges drained by Number to Drain. Non-recharging items drained of all their charges are destroyed.
Known values for 'Item Type' are:
0 Magical items excluding weapons
1 Magical items including weapons