I'm not really sure what I'd do if I were you. Normally I leave wonders and special buildings intact (though I was seriously considering looting the Royal Makedonian Tombs when playing as KH). It depends on your approach. So far, your approach seems to be raiding, so getting in and out quickly is key. Since it sounds as though you wish to return and retake the city with a larger force, I would leave the ruins intact (though I'd destroy any recruitment centers and governments they have before withdrawing). But if you're going to focus on other regions of the Seleucid Empire and are going for an aggressive approach, by all means, destroy it.

By the way, does anyone know how much the special wonders/structures really benefit?