Once a sprite gets small, there's not a lot you can do to prevent pixelation (there are, after all, very few pixels). This is a concern with vector art because you design in a pixel-free environment -- you have to make design choices that will scale well when in pixel form (e.g. bold lines, no tiny details).
It's possible that down sampling algorithms in other software will do a bit better, in which case exporting high res and then batch scaling would be the way to go!