Patriots aren't the answer to Shaheds, but that's the wrong way to look at it. You don't compare the price of an APS charge with the price of an RPG. You don't spec your soldiers' ballistic plates by aiming to bring their cost down below the cost of the bullet you hope it'll stop. The plate is replaceable, the soldier's heart isn't, you sacrifice the thing you're happy to lose to save the thing you want to keep.
They're not happy they shot down $50k of drone, they're happy they shot down 50 kg of explosives that was going to strike a power station, it's not a hard trade to make.