How do I apply effects to a layer at its current resolution (scaled up by the layer's scale property) instead of its original resolution?
Well, the answer to the question in your title is to apply the CC Slant effect to an adjustment layer above your (scaled-up) sprite layer. The adjustment layer will have the same resolution as the comp.

But based on the description below the title, I'm not 100% confident this is what you want. Let me know.